Parameter	Value
Version	1.3.0.5
Fixed modifications	Carbamidomethyl (C)
Randomize	False
Special AAs	KR
Include contaminants	True
MS/MS tol. (FTMS)	20 ppm
Top MS/MS peaks per 100 Da. (FTMS)	10
MS/MS deisotoping (FTMS)	True
MS/MS tol. (ITMS)	0.5 Da
Top MS/MS peaks per 100 Da. (ITMS)	6
MS/MS deisotoping (ITMS)	False
MS/MS tol. (TOF)	0.1 Da
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)	6
MS/MS deisotoping (Unknown)	False
Peptide FDR	0.01
Max. peptide PEP	1
Protein FDR	0.01
Site FDR	0.01
Use Normalized Ratios For Occupancy	True
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);DesBiotin(K)
Peptides used for protein quantification	Razor
Discard unmodified counterpart peptides	True
Min. ratio count	2
Lfq min. ratio count	2
Site quantification	Use least modified peptide
Re-quantify	False
Keep low-scoring versions of identified peptides	No
Label-free protein quantification	False
iBAQ	False
iBAQ log fit	True
MS/MS recalibration	False
Match between runs	False
Find dependent peptides	False
Fasta file	C:\MaxQuant 1.3.0.5\database\uniprot.HUMAN.2011_11.fasta
First search fasta file	C:\MaxQuant 1.3.0.5\database\human.first.search.fasta
Labeled amino acid filtering	True
Site tables	DesBiotin(K)Sites.txt;Oxidation (M)Sites.txt
Cut peaks	True
Randomize	False
Special AAs	KR
Include contaminants	True
RT shift	False
Advanced ratios	False
AIF correlation	0.8
First pass AIF correlation	0.8
AIF topx	50
AIF min mass	0
AIF SIL weight	4
AIF ISO weight	2
AIF iterative	False
AIF threshold FDR	0.01