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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 MaSu
Machine name SADDALA
Date of writing 08/14/2018 15:36:19
Fixed modifications Carbamidomethyl (C)
Include contaminants True
PSM FDR 0.01
XPSM 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 All
Discard unmodified counterpart peptides True
Label min. ratio count 2
Use delta score False
iBAQ False
iBAQ log fit False
Match between runs False
Find dependent peptides False
Fasta file E:\Proteomic softwares\MaxQuant\contaminants.fasta;E:\Proteomic softwares\MaxQuant\uniprot-human.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
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