Parameter	Value
Version	1.5.9.3
User name	maxquant
Machine name	PCMANN174
Date of writing	06/07/2017 13:38:55
Fixed modifications	Carbamidomethyl (C)
Include contaminants	True
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
Label 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:\fasta\2015\UP000005640_9606.fasta;E:\fasta\2015\UP000005640_9606_additional.fasta
Decoy mode	revert
Include contaminants	True
Advanced ratios	True
Fixed andromeda index folder	
Temporary folder	
Combined folder location	
Second peptides	True
Stabilize large LFQ ratios	True
Separate LFQ in parameter groups	False
Require MS/MS for LFQ comparisons	True
Calculate peak properties	False
Main search max. combinations	200
Advanced site intensities	True
Write msScans table	True
Write msmsScans table	True
Write ms3Scans table	True
Write allPeptides table	True
Write mzRange table	True
Max. peptide mass [Da]	4600
Min. peptide length for unspecific search	8
Max. peptide length for unspecific search	25
Razor protein FDR	True
Disable MD5	False
Max mods in site table	3
Match unidentified features	False
Taxonomy level	Species
Top 3	False
Match between runs FDR	False
RT shift	False
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
AIF MS/MS tolerance [ppm]	0
AIF Second pass	False
Epsilon score for mutations	
Evaluate variant peptides separately	True
Evaluate proteogenomic peptides separately	True
AVALON	False
De-novo sequencing	False
De-novo include variable modifications	True
Mass difference search	False
Mass difference search modifications	System.String[]
Variation mode	None
Variation parse rule	
Custom protein quantification	False
Custom protein quantification file	
Split protein groups by taxonomy ID	False
Show centroid mass differences	False
Show isotope mass differences	False
Connect MS/MS	False
Composition prediction	None
Verbose table column headers	False
MS/MS tol. (FTMS)	20 ppm
Top MS/MS peaks per Da interval. (FTMS)	12
Da interval. (FTMS)	100
MS/MS deisotoping (FTMS)	True
MS/MS deisotoping tolerance (FTMS)	7
MS/MS deisotoping tolerance unit (FTMS)	ppm
MS/MS higher charges (FTMS)	True
MS/MS water loss (FTMS)	True
MS/MS ammonia loss (FTMS)	True
MS/MS dependent losses (FTMS)	True
MS/MS recalibration (FTMS)	False
MS/MS de novo tolerance (FTMS)	10
MS/MS de novo tolerance unit (FTMS)	ppm
MS/MS tol. (ITMS)	0.5 Da
Top MS/MS peaks per Da interval. (ITMS)	8
Da interval. (ITMS)	100
MS/MS deisotoping (ITMS)	False
MS/MS deisotoping tolerance (ITMS)	0.15
MS/MS deisotoping tolerance unit (ITMS)	Da
MS/MS higher charges (ITMS)	True
MS/MS water loss (ITMS)	True
MS/MS ammonia loss (ITMS)	True
MS/MS dependent losses (ITMS)	True
MS/MS recalibration (ITMS)	False
MS/MS de novo tolerance (ITMS)	0.25
MS/MS de novo tolerance unit (ITMS)	Da
MS/MS tol. (TOF)	40 ppm
Top MS/MS peaks per Da interval. (TOF)	10
Da interval. (TOF)	100
MS/MS deisotoping (TOF)	True
MS/MS deisotoping tolerance (TOF)	0.01
MS/MS deisotoping tolerance unit (TOF)	Da
MS/MS higher charges (TOF)	True
MS/MS water loss (TOF)	True
MS/MS ammonia loss (TOF)	True
MS/MS dependent losses (TOF)	True
MS/MS recalibration (TOF)	False
MS/MS de novo tolerance (TOF)	0.02
MS/MS de novo tolerance unit (TOF)	Da
MS/MS tol. (Unknown)	0.5 Da
Top MS/MS peaks per Da interval. (Unknown)	8
Da interval. (Unknown)	100
MS/MS deisotoping (Unknown)	False
MS/MS deisotoping tolerance (Unknown)	0.15
MS/MS deisotoping tolerance unit (Unknown)	Da
MS/MS higher charges (Unknown)	True
MS/MS water loss (Unknown)	True
MS/MS ammonia loss (Unknown)	True
MS/MS dependent losses (Unknown)	True
MS/MS recalibration (Unknown)	False
MS/MS de novo tolerance (Unknown)	0.25
MS/MS de novo tolerance unit (Unknown)	Da
Site tables	Oxidation (M)Sites.txt