Parameter	Value
Version	2.1.0.0
User name	liqer
Machine name	DESKTOP-LA4DBJ8
Date of writing	02/22/2023 10:52:58
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
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	1
Use delta score	False
iBAQ	True
iBAQ log fit	True
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	False
Fasta file	D:\Database\uniprot-download_true_format_fasta_query_human_ribosomal_proteins-20220829.fasta
Decoy mode	revert
Include contaminants	True
Advanced ratios	True
Fixed andromeda index 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	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
Epsilon score for mutations	
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 water loss (FTMS for cross link)	False
MS/MS ammonia loss (FTMS)	True
MS/MS ammonia loss (FTMS for cross link)	False
MS/MS dependent losses (FTMS)	True
MS/MS recalibration (FTMS)	False
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 water loss (ITMS for cross link)	False
MS/MS ammonia loss (ITMS)	True
MS/MS ammonia loss (ITMS for cross link)	False
MS/MS dependent losses (ITMS)	True
MS/MS recalibration (ITMS)	False
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 water loss (TOF for cross link)	False
MS/MS ammonia loss (TOF)	True
MS/MS ammonia loss (TOF for cross link)	False
MS/MS dependent losses (TOF)	True
MS/MS recalibration (TOF)	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 water loss (Unknown for cross link)	False
MS/MS ammonia loss (Unknown)	True
MS/MS ammonia loss (Unknown for cross link)	False
MS/MS dependent losses (Unknown)	True
MS/MS recalibration (Unknown)	False
Cross linking type	NonCleavable
Crosslinker	BS3
Min. matches	3
Min. length for a paired-peptide sequence	6
Min. score for cross-linked peptides	0
Min. score for other crosslink products	0
Min. partial score for cross-linked peptides	10
Include intensity based strategy	True
Less stringent delta-mass prec. determination	False
Top n intense peaks	3
Separate protein intra- and inter-cross links	True
Max. hydrolyzed mono-peptide links	1
Max. linked mono-peptide links	1
Max. hydrolyzed di-peptide links	0
Max. linked di-peptide links	1
Site tables	Oxidation (M)Sites.txt
