Proteomics: MaxQuant and MSstats for the analysis of label-free data

Associated Tutorial

Tutorial Author(s): Melanie Föll, Matthias Fahrner

Inputs

ID	Name	Description	Type
Evidence	Evidence	n/a	File
Protein Groups	Protein Groups	n/a	File
annotation file	annotation file	n/a	File
comparison matrix	comparison matrix	n/a	File

Steps

ID	Name	Description
4	Select	Grep1
5	Select	Grep1
6	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0
7	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0
8	MSstats	toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/4.0.0+galaxy1
9	Summary Statistics	Summary_Statistics1
10	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0
11	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0
12	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
13	Filter	Filter1
14	Filter	Filter1
15	Filter	Filter1
16	Filter	Filter1
17	Filter	Filter1
18	Cut	Cut1
19	Cut	Cut1
20	Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy0
21	Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy0
22	UniProt	toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.5
23	heatmap2	toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1
24	heatmap2	toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1
25	UniProt	toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.5
26	FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
27	FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1

Outputs

ID	Name	Description	Type
select protein groups	select protein groups	n/a	File
select protein evidence	select protein evidence	n/a	File
protein groups input for MSstats	protein groups input for MSstats	n/a	File
evidence input for MSstats	evidence input for MSstats	n/a	File
replaced sample quantification matrix	replaced sample quantification matrix	n/a	File
replaced comparison result	replaced comparison result	n/a	File
significant proteins	significant proteins	n/a	File
metastasized filtered	metastasized filtered	n/a	File
rdeb filtered	rdeb filtered	n/a	File
significant metastasized	significant metastasized	n/a	File
significant rdeb	significant rdeb	n/a	File
metastasized cut	metastasized cut	n/a	File
rdeb cut	rdeb cut	n/a	File
metastasized join	metastasized join	n/a	File
rdeb join	rdeb join	n/a	File
metastasized uniprot	metastasized uniprot	n/a	File
Upregulated proteins in metastasized cSCC	Upregulated proteins in metastasized cSCC	n/a	File
Upregulated proteins in RDEB cSCC	Upregulated proteins in RDEB cSCC	n/a	File
rdeb uniprot	rdeb uniprot	n/a	File