Parameter	Value
Version	1.1.1.25
Peptide FDR	0.01
Max. peptide PEP	1
Protein FDR	0.01
Site FDR	0.01
Apply site FDR separately	True
Min. peptide Length	6
Min. score	0
Min. unique peptides	0
Min. razor peptides	1
Min. peptides	1
Use only unmodified peptides and	True
Modifications included in protein quantification	Oxidation (M);Acetyl (Protein N-term)
Peptides used for protein quantification	Razor
Discard unmodified counterpart peptides	True
Min. ratio count	2
Site quantification	Use least modified peptide
Re-quantify	True
Keep low-scoring versions of identified peptides	True
Label-free protein quantification	False
iBAQ	False
iBAQ log fit	True
Match between runs	True
Time window	True
Find dependent peptides	False
Fasta file	F:\Documents and Settings\Falko\Desktop\Fasta-Databases\uniprot_human_2010-10.fasta
First search fasta file	F:\Documents and Settings\Falko\Desktop\Fasta-Databases\uniprot_human_2010-10.fasta
Experimental design file	F:\Documents and Settings\Falko\Desktop\MQ_Projects\Luxi\to gagri\Mix4_TiO2\combined\experimentalDesignTemplate.txt
Mass filtering	True
Labeled amino acid filtering	True
Site tables	Oxidation (M)Sites.txt;Phospho (STY)Sites.txt
Calculate PIF	False
Cut peaks	True
Variable modifications	Oxidation (M);Acetyl (Protein N-term);Phospho (STY)
Fixed modifications	Carbamidomethyl (C)
Randomize	False
Special AAs	KR
Include contaminants	True
Multiplicity	1
First search ppm tol	20
MS/MS tol. (CID)	0.5 Da
Top MS/MS peaks per 100 Da. (CID)	6
MS/MS deisotoping (CID)	False
MS/MS tol. (HCD)	20 ppm
Top MS/MS peaks per 100 Da. (HCD)	10
MS/MS deisotoping (HCD)	True
MS/MS tol. (Unknown)	0.5 Da
Top MS/MS peaks per 100 Da. (Unknown)	6
MS/MS deisotoping (Unknown)	False
AIF correlation	0.8
AIF topx	50
AIF topx corr	False
AIF min mass	0
AIF SIL weight	4
AIF ISO weight	2