A Pipeline for Peptide Detection Using Multiple Decoys

Syamand Hasam; Kristen Emery; William Stafford Noble; Uri Keich

doi:10.1007/978-1-0716-1967-4_2

A Pipeline for Peptide Detection Using Multiple Decoys

Methods Mol Biol. 2023:2426:25-34. doi: 10.1007/978-1-0716-1967-4_2.

Authors

Syamand Hasam¹, Kristen Emery¹, William Stafford Noble², Uri Keich³

Affiliations

¹ University of Sydney, Sydney, NSW, Australia.
² University of Washington, Seattle, WA, USA.
³ University of Sydney, Sydney, NSW, Australia. uri.keich@sydney.edu.au.

PMID: 36308683
DOI: 10.1007/978-1-0716-1967-4_2

Abstract

Target-decoy competition has been commonly used for over a decade to control the false discovery rate when analyzing tandem mass spectrometry (MS/MS) data. We recently developed a framework that uses multiple decoys to increase the number of detected peptides in MS/MS data. Here, we present a pipeline of Apache licensed, open-source software that allows the user to readily take advantage of our framework.

Keywords: FDR control; Multiple decoys; Peptide detection; Tandem mass spectrometry.

MeSH terms

Algorithms
Databases, Protein
Peptides / chemistry
Proteomics* / methods
Software
Tandem Mass Spectrometry* / methods

Substances

Peptides