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parameters.txt
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parameters.txt
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Parameter Value
Version 1.6.1.0
User name betzalex
Machine name UTO-BETZALEX-PC
Date of writing 03/11/2018 12:12:45
Fixed modifications Carbamidomethyl (C)
Include contaminants True
PSM FDR 0.01
XPSM FDR 0
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 False
Peptides used for protein quantification Razor
Discard unmodified counterpart peptides True
Label min. ratio count 2
Use delta score False
iBAQ True
iBAQ log fit True
Match between runs True
Matching time window [min] 0.7
Alignment time window [min] 20
Find dependent peptides True
Dependent peptide FDR 0.01
Mass bin size 0.0065
Fasta file E:\polybox\projects\mixTox\genomic\cre_all_proteins.fa
Decoy mode revert
Include contaminants True
Advanced ratios True
Fixed andromeda index folder E:\db_indices\andromeda
Temporary folder E:\temp
Combined folder location E:\data\prot_pipe_out
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
LFQ norm for sites and peptides False
Write msScans table True
Write msmsScans table True
Write ms3Scans table True
Write allPeptides table True
Write mzRange table True
Write pasefMsmsScans table True
Write accumulatedPasefMsmsScans 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
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. (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 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 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
Site tables Oxidation (M)Sites.txt