================================================================================
Search name: Bacillus_Curcumin_TP_10
Search description: -
Search date: 11/09/2013 09:16:58
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_10.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_11
Search description: -
Search date: 11/09/2013 09:27:03
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_11.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_12
Search description: -
Search date: 11/09/2013 10:27:41
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_12.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_13
Search description: -
Search date: 11/09/2013 10:36:15
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_13.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_15
Search description: -
Search date: 11/09/2013 10:43:18
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_15.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_16
Search description: -
Search date: 11/09/2013 11:19:40
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_16.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_17
Search description: -
Search date: 11/09/2013 11:55:00
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_17.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_18
Search description: -
Search date: 11/09/2013 12:39:04
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_18.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_19
Search description: -
Search date: 11/09/2013 12:49:47
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_19.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_20
Search description: -
Search date: 11/11/2013 09:16:24
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_20.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_21
Search description: -
Search date: 11/11/2013 09:47:12
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_21.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_22
Search description: -
Search date: 11/11/2013 09:54:55
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_22.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_23
Search description: -
Search date: 11/11/2013 11:59:18
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_23.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_24
Search description: -
Search date: 11/11/2013 12:23:00
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_24.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_6
Search description: -
Search date: 11/12/2013 09:51:29
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(5) Annotation
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_6.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 5: Annotation
------------------------------------------------------------------------------
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_7
Search description: -
Search date: 11/09/2013 08:38:41
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_7.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_8
Search description: -
Search date: 11/09/2013 10:22:30
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_8.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_Curcumin_TP_9
Search description: -
Search date: 11/09/2013 08:50:07
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s):
G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_10.raw
G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_11.raw
G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_8.raw
G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_Curcumin_TP_9.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_offgel_1
Search description: -
Search date: 11/08/2013 17:58:23
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_offgel_1.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_offgel_2
Search description: -
Search date: 11/08/2013 18:04:34
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_offgel_2.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_offgel_3
Search description: -
Search date: 11/08/2013 18:10:33
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_offgel_3.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_offgel_4
Search description: -
Search date: 11/08/2013 18:15:53
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_offgel_4.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000
================================================================================
Search name: Bacillus_offgel_5
Search description: -
Search date: 11/08/2013 18:30:09
================================================================================
The pipeline tree:
------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) SEQUEST
|-(3) Target Decoy PSM Validator
|-(4) Reporter Ions Quantifier
------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------
Input Data:
-----------------------------
File Name(s): G:\Jaipal\Experimental results\MALDI and LC-MS data\IOB data\Curcumin\Bacillus_offgel_5.raw
------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------
1. General Settings:
-----------------------------
Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True
2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit: 0
Upper RT Limit: 0
First Scan: 0
Last Scan: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 350 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1
3. Scan Event Filters:
-----------------------------
Mass Analyzer: Is FTMS
MS Order: Is MS2
Activation Type: Is HCD
Min. Collision Energy: 0
Max. Collision Energy: 100
Scan Type: Is Full
Ionization Source: Is Nanospray
Polarity Mode: Is +
4. Peak Filters:
-----------------------------
S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements: Automatic
Unrecognized Mass Analyzer Replacements: FTMS
Unrecognized MS Order Replacements: MS2
Unrecognized Activation Type Replacements: HCD
Unrecognized Polarity Replacements: +
6. Just for Testing:
-----------------------------
Precursor Clipping Range Before: 2.5 Da
Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------------------
Processing node 2: SEQUEST
------------------------------------------------------------------------------
1. Input Data:
-----------------------------
Protein Database: UniProt.fasta
Enzyme Name: Trypsin (Full)
Maximum Missed Cleavage Sites: 1
1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered: 500
Maximum Peptides Output: 10
Calculate Probability Scores: False
Absolute XCorr Threshold: 0.4
Fragment Ion Cutoff Percentage: 0.1
Peptide Without Protein XCorr Threshold: 1.5
1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide: 100
Protein Relevance Threshold: 1.5
Peptide Relevance Factor: 0.4
2. Tolerances:
-----------------------------
Precursor Mass Tolerance: 20 ppm
Fragment Mass Tolerance: 0.1 Da
Use Average Precursor Mass: False
Use Average Fragment Masses: False
3. Ion Series:
-----------------------------
Use Neutral Loss a Ions: True
Use Neutral Loss b Ions: True
Use Neutral Loss y Ions: True
Weight of a Ions: 0
Weight of b Ions: 1
Weight of c Ions: 0
Weight of x Ions: 0
Weight of y Ions: 1
Weight of z Ions: 0
4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide: 4
1. Dynamic Modification: Oxidation / +15.995 Da (M)
5. Static Modifications:
-----------------------------
Peptide N-Terminus: iTRAQ4plex / +144.102 Da (Any N-Terminus)
2. Static Modification: iTRAQ4plex / +144.102 Da (K)
------------------------------------------------------------------------------
Processing node 3: Target Decoy PSM Validator
------------------------------------------------------------------------------
1. Decoy Database Search:
-----------------------------
Target FDR (Strict): 0.01
Target FDR (Relaxed): 0.05
------------------------------------------------------------------------------
Processing node 4: Reporter Ions Quantifier
------------------------------------------------------------------------------
1. Quantification Method:
-----------------------------
Quantification Method: iTRAQ 4plex (Thermo Scientific Instruments) (Custom)
2. Peak Integration:
-----------------------------
Integration Tolerance: 20 ppm
Integration Method: Most Confident Centroid
3. Scan Event Filters:
-----------------------------
Mass Analyzer: FTMS
MS Order: MS2
Activation Type: HCD
Min. Collision Energy: 0
Max. Collision Energy: 1000