Mercurial > repos > galaxyp > maxquant

comparison test-data/single/combined/txt/parameters.txt @ 1:8bac3cc5c5de draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Sat, 20 Jul 2019 05:01:05 -0400
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0:d4b6c9eae635 1:8bac3cc5c5de
1 Parameter Value
2 Version 1.6.3.4
3 User name dglaetzer
4 Machine name FPROT-BEAST
5 Date of writing 04/04/2019 17:32:37
6 Include contaminants True
7 PSM FDR 0.01
8 PSM FDR Crosslink 0.01
9 Protein FDR 0.01
10 Site FDR 0.01
11 Use Normalized Ratios For Occupancy True
12 Min. peptide Length 7
13 Min. score for unmodified peptides 0
14 Min. score for modified peptides 40
15 Min. delta score for unmodified peptides 0
16 Min. delta score for modified peptides 6
17 Min. unique peptides 0
18 Min. razor peptides 1
19 Min. peptides 1
20 Use only unmodified peptides and True
21 Modifications included in protein quantification Oxidation (M)
22 Peptides used for protein quantification Razor
23 Discard unmodified counterpart peptides True
24 Label min. ratio count 2
25 Use delta score False
26 iBAQ False
27 iBAQ log fit False
28 Match between runs False
29 Find dependent peptides False
30 Fasta file D:\fasta\bsa.fasta
31 Decoy mode revert
32 Include contaminants True
33 Advanced ratios True
34 Fixed andromeda index folder
35 Temporary folder
36 Combined folder location
37 Second peptides True
38 Stabilize large LFQ ratios True
39 Separate LFQ in parameter groups False
40 Require MS/MS for LFQ comparisons True
41 Calculate peak properties False
42 Main search max. combinations 200
43 Advanced site intensities True
44 Write msScans table False
45 Write msmsScans table True
46 Write ms3Scans table True
47 Write allPeptides table True
48 Write mzRange table True
49 Write pasefMsmsScans table True
50 Write accumulatedPasefMsmsScans table True
51 Max. peptide mass [Da] 4600
52 Min. peptide length for unspecific search 8
53 Max. peptide length for unspecific search 25
54 Razor protein FDR True
55 Disable MD5 False
56 Max mods in site table 3
57 Match unidentified features False
58 Epsilon score for mutations
59 Evaluate variant peptides separately True
60 Variation mode None
61 MS/MS tol. (FTMS) 20 ppm
62 Top MS/MS peaks per Da interval. (FTMS) 12
63 Da interval. (FTMS) 100
64 MS/MS deisotoping (FTMS) True
65 MS/MS deisotoping tolerance (FTMS) 7
66 MS/MS deisotoping tolerance unit (FTMS) ppm
67 MS/MS higher charges (FTMS) True
68 MS/MS water loss (FTMS) True
69 MS/MS ammonia loss (FTMS) True
70 MS/MS dependent losses (FTMS) True
71 MS/MS recalibration (FTMS) False
72 MS/MS tol. (ITMS) 0.5 Da
73 Top MS/MS peaks per Da interval. (ITMS) 8
74 Da interval. (ITMS) 100
75 MS/MS deisotoping (ITMS) False
76 MS/MS deisotoping tolerance (ITMS) 0.15
77 MS/MS deisotoping tolerance unit (ITMS) Da
78 MS/MS higher charges (ITMS) True
79 MS/MS water loss (ITMS) True
80 MS/MS ammonia loss (ITMS) True
81 MS/MS dependent losses (ITMS) True
82 MS/MS recalibration (ITMS) False
83 MS/MS tol. (TOF) 40 ppm
84 Top MS/MS peaks per Da interval. (TOF) 10
85 Da interval. (TOF) 100
86 MS/MS deisotoping (TOF) True
87 MS/MS deisotoping tolerance (TOF) 0.01
88 MS/MS deisotoping tolerance unit (TOF) Da
89 MS/MS higher charges (TOF) True
90 MS/MS water loss (TOF) True
91 MS/MS ammonia loss (TOF) True
92 MS/MS dependent losses (TOF) True
93 MS/MS recalibration (TOF) False
94 MS/MS tol. (Unknown) 0.5 Da
95 Top MS/MS peaks per Da interval. (Unknown) 8
96 Da interval. (Unknown) 100
97 MS/MS deisotoping (Unknown) False
98 MS/MS deisotoping tolerance (Unknown) 0.15
99 MS/MS deisotoping tolerance unit (Unknown) Da
100 MS/MS higher charges (Unknown) True
101 MS/MS water loss (Unknown) True
102 MS/MS ammonia loss (Unknown) True
103 MS/MS dependent losses (Unknown) True
104 MS/MS recalibration (Unknown) False
105 Site tables Oxidation (M)Sites.txt