Mercurial > repos > galaxyp > maxquant

comparison test-data/mqpar/txt/parameters.txt @ 15:97a7f34fcb6a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:24:23 +0000
parents
children 8934bc76bb52
comparison
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14:e42225f8a659 15:97a7f34fcb6a
1 Parameter Value
2 Version 1.6.17.0
3 User name niko
4 Machine name DESKTOP-I3UDKML
5 Date of writing 08/05/2021 17:10:11
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);Acetyl (Protein N-term)
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 /tmp/tmpfjtbnut8/files/c/c/5/dataset_cc5df07a-ee7c-4aa9-a851-1d22973dc663.dat
31 Decoy mode revert
32 Include contaminants True
33 Advanced ratios True
34 Fixed andromeda index folder
35 Combined folder location
36 Second peptides True
37 Stabilize large LFQ ratios True
38 Separate LFQ in parameter groups False
39 Require MS/MS for LFQ comparisons True
40 Calculate peak properties False
41 Main search max. combinations 200
42 Advanced site intensities True
43 Write msScans table False
44 Write msmsScans table True
45 Write ms3Scans table True
46 Write allPeptides table True
47 Write mzRange table True
48 Write DIA fragments table False
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) 20 ppm
95 Top MS/MS peaks per Da interval. (Unknown) 12
96 Da interval. (Unknown) 100
97 MS/MS deisotoping (Unknown) True
98 MS/MS deisotoping tolerance (Unknown) 7
99 MS/MS deisotoping tolerance unit (Unknown) ppm
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