Proteomics: MaxQuant and MSstats LFQ workflow
3.0

Workflow Type: Galaxy

MaxQuant and MSstats for the analysis of label-free data

Associated Tutorial

This workflows is part of the tutorial Proteomics: MaxQuant and MSstats LFQ workflow, available in the GTN

Thanks to...

Tutorial Author(s): Melanie Föll, Matthias Fahrner

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
annotation file #main/annotation file n/a
  • File
comparison matrix #main/comparison matrix n/a
  • File
fasta protein database #main/fasta protein database n/a
  • File
raw files #main/raw files n/a
  • array containing
    • File

Steps

ID Name Description
4 MaxQuant toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4
5 Select Grep1
6 Select Grep1
7 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
8 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
9 MSstats toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1
10 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6
11 Summary Statistics Summary_Statistics1
12 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
13 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
14 Filter Filter1
15 Filter Filter1
16 Filter Filter1
17 Filter Filter1
18 Filter Filter1
19 Cut Cut1
20 Cut Cut1
21 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
22 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
23 heatmap2 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1
24 UniProt toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2
25 heatmap2 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1
26 UniProt toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2
27 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
28 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_15 #main/_anonymous_output_15 n/a
  • File
_anonymous_output_16 #main/_anonymous_output_16 n/a
  • File
_anonymous_output_17 #main/_anonymous_output_17 n/a
  • File
_anonymous_output_18 #main/_anonymous_output_18 n/a
  • File
_anonymous_output_19 #main/_anonymous_output_19 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_20 #main/_anonymous_output_20 n/a
  • File
_anonymous_output_21 #main/_anonymous_output_21 n/a
  • File
_anonymous_output_22 #main/_anonymous_output_22 n/a
  • File
_anonymous_output_23 #main/_anonymous_output_23 n/a
  • File
_anonymous_output_24 #main/_anonymous_output_24 n/a
  • File
_anonymous_output_25 #main/_anonymous_output_25 n/a
  • File
_anonymous_output_26 #main/_anonymous_output_26 n/a
  • File
_anonymous_output_27 #main/_anonymous_output_27 n/a
  • File
_anonymous_output_28 #main/_anonymous_output_28 n/a
  • File
_anonymous_output_29 #main/_anonymous_output_29 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_30 #main/_anonymous_output_30 n/a
  • File
_anonymous_output_31 #main/_anonymous_output_31 n/a
  • File
_anonymous_output_32 #main/_anonymous_output_32 n/a
  • File
_anonymous_output_33 #main/_anonymous_output_33 n/a
  • File
_anonymous_output_34 #main/_anonymous_output_34 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

3.0 (earliest) Created 25th Jun 2024 at 11:14 by Helena Rasche

Added/updated 4 files


Open master f09523a
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Views: 363   Downloads: 80

Created: 25th Jun 2024 at 11:14

Last updated: 25th Jun 2024 at 11:14

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