Parameter	Value
Version	1.5.3.8
User name	USER
Machine name	P8H77MLE1011213
Date of writing	11/16/2016 09:48:20
Fixed modifications	Carbamidomethyl (C)
Decoy mode	revert
Special AAs	KR
Include contaminants	True
MS/MS tol. (FTMS)	20 ppm
Top MS/MS peaks per 100 Da. (FTMS)	12
MS/MS deisotoping (FTMS)	True
MS/MS tol. (ITMS)	0.5 Da
Top MS/MS peaks per 100 Da. (ITMS)	8
MS/MS deisotoping (ITMS)	False
MS/MS tol. (TOF)	40 ppm
Top MS/MS peaks per 100 Da. (TOF)	10
MS/MS deisotoping (TOF)	True
MS/MS tol. (Unknown)	0.5 Da
Top MS/MS peaks per 100 Da. (Unknown)	8
MS/MS deisotoping (Unknown)	False
PSM FDR	0.01
Protein FDR	0.01
Site FDR	0.01
Use Normalized Ratios For Occupancy	True
Min. peptide Length	7
Min. score for unmodified peptides	0
Min. score for modified peptides	40
Min. delta score for unmodified peptides	0
Min. delta score for modified peptides	6
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
Use delta score	False
iBAQ	False
iBAQ log fit	False
Match between runs	True
Matching time window [min]	0.7
Alignment time window [min]	20
Find dependent peptides	False
Fasta file	E:\Sequence\SWISSPROT-Human-CANONICAL-2016_05.fasta
Labeled amino acid filtering	True
Site tables	Oxidation (M)Sites.txt;Phospho (STY)Sites.txt
Decoy mode	revert
Special AAs	KR
Include contaminants	True
RT shift	False
Advanced ratios	True
AIF correlation	0
First pass AIF correlation	0
AIF topx	0
AIF min mass	0
AIF SIL weight	0
AIF ISO weight	0
AIF iterative	False
AIF threshold FDR	0