Parameter	Value
Version	2.0.1.0
Include contaminants	TRUE
PSM FDR	0.01
PSM FDR Crosslink	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
Fixed modification
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
Match ion mobility window [indices]	0.05
Alignment time window [min]	20
Alignment ion mobility window [indices]	1
Find dependent peptides	TRUE
Dependent peptide FDR	0.01
Mass bin size	0.0065
Decoy mode	revert
Include contaminants	TRUE
Advanced ratios	TRUE
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	FALSE
Write msmsScans table	TRUE
Write ms3Scans table	TRUE
Write allPeptides table	TRUE
Write mzRange table	TRUE
Write DIA fragments table	FALSE
Write DIA fragments quant table	FALSE
Write pasefMsmsScans table	TRUE
Write accumulatedMsmsScans 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
Evaluate variant peptides separately	TRUE
Variation mode	None
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 tol. (Unknown)	20 ppm
Top MS/MS peaks per Da interval. (Unknown)	12
Da interval. (Unknown)	100
MS/MS deisotoping (Unknown)	TRUE
MS/MS deisotoping tolerance (Unknown)	7
MS/MS deisotoping tolerance unit (Unknown)	ppm
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
Site tables	Deamidation (NQ)Sites.txt;Oxidation (M)Sites.txt;Phospho (STY)Sites.txt
Enzyme	Trypsin/P
Enzyme mode	Specific
Use enzyme first search	FALSE
Use variable modifications first search	FALSE
Requantify	TRUE
Multiplicity	2
Max. missed cleavages	2
Max. labeled AAs	3
Labels0
Labels1	Arg10;Lys8
LC-MS run type	Standard