clinicalmp-verification/main
v0.1

Workflow Type: Galaxy

In proteomics research, verifying detected peptides is essential for ensuring data accuracy and biological relevance. This tutorial continues from the clinical metaproteomics discovery workflow, focusing on verifying identified microbial peptides using the PepQuery tool.

SEEK ID: https://workflowhub.eu/workflows/1218?version=1

Inputs

ID	Name	Description	Type
Distinct Peptides for PepQuery	Distinct Peptides for PepQuery	Microbial peptides that will be used for PepQuery2 analysis.	File
MaxQuant peptide report	MaxQuant peptide report	Peptide report from MaxQuant search.	File
SGPS peptide report	SGPS peptide report	The peptide report from SearchGUI/PeptideShaker.	File
MS) datasets	Tandem Mass Spectrometry (MS/MS) datasets	The MGF files from mass spectrometry data.	File[]

Steps

ID	Name	Description
0	Human UniProt Isoforms FASTA	toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4
1	cRAP	toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4
6	Human UniProt Isoforms cRAP FASTA	toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
7	SGPS Cut	Cut1
8	MQ Cut	Cut1
9	PepQuery2	toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy2
10	SGPS Remove Beginner	Remove beginning1
11	MQ Remove Beginner	Remove beginning1
12	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
13	Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
14	Filter	Filter1
15	Filter Remove beginning	Remove beginning1
16	FRB Cut	Cut1
17	Peptide and Protein from Peptide Reports	toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
18	PPPR Remove beginning	Remove beginning1
19	Group	Grouping1
20	Uniprot ID from verified Peptides	toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
21	UniProt	toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0
22	Quantitation Database for MaxQuant	toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0

Outputs

ID	Name	Description	Type
Human UniProt+Isoforms FASTA	Human UniProt+Isoforms FASTA	n/a	File
cRAP	cRAP	n/a	File
Human UniProt+Isoforms+cRAP FASTA	Human UniProt+Isoforms+cRAP FASTA	n/a	File
Peptide and Protein from Peptide Reports	Peptide and Protein from Peptide Reports	n/a	File
Uniprot ID from verified Peptides	Uniprot ID from verified Peptides	n/a	File
Quantitation Database for MaxQuant	Quantitation Database for MaxQuant	n/a	File