================================================================================ Search name: IITB_B_sub_cur_1 Search description: - Search date: 11/02/2013 09:01:26 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_10 Search description: - Search date: 11/01/2013 23:04:19 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_11 Search description: - Search date: 11/01/2013 23:10:47 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_12 Search description: - Search date: 11/01/2013 23:13:46 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_13 Search description: - Search date: 11/01/2013 23:18:46 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_14 Search description: - Search date: 11/02/2013 10:04:40 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_14.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: IITB_B_sub_cur_15 Search description: - Search date: 11/02/2013 08:27:46 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_2 Search description: - Search date: 11/01/2013 22:13:27 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_3 Search description: - Search date: 11/02/2013 09:21:07 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_4 Search description: - Search date: 11/02/2013 08:31:35 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_5 Search description: - Search date: 11/02/2013 10:28:33 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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

================================================================================ Search name: IITB_B_sub_cur_6 Search description: - Search date: 11/01/2013 22:45:21 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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 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: IITB_B_sub_cur_7 Search description: - Search date: 11/01/2013 22:54:56 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_8 Search description: - Search date: 11/02/2013 10:49:28 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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: IITB_B_sub_cur_9 Search description: - Search date: 11/01/2013 22:59:36 ================================================================================ 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\Three drugs raw data\IITB_B_sub_cur_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