Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets

Camacho, Oscar M, Ramsbottom, Kerry A ORCID: 0000-0002-7432-9293, Collins, Andrew ORCID: 0000-0003-0507-6912 and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2023) Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets. JOURNAL OF PROTEOME RESEARCH, 22 (6). pp. 1828-1842.

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Official URL: http://dx.doi.org/10.1021/acs.jproteome.2c00823

Abstract

Phosphorylation is a post-translational modification of great interest to researchers due to its relevance in many biological processes. LC-MS/MS techniques have enabled high-throughput data acquisition, with studies claiming identification and localization of thousands of phosphosites. The identification and localization of phosphosites emerge from different analytical pipelines and scoring algorithms, with uncertainty embedded throughout the pipeline. For many pipelines and algorithms, arbitrary thresholding is used, but little is known about the actual global false localization rate in these studies. Recently, it has been suggested to use decoy amino acids to estimate global false localization rates of phosphosites, among the peptide-spectrum matches reported. Here, we describe a simple pipeline aiming to maximize the information extracted from these studies by objectively collapsing from peptide-spectrum match to the peptidoform-site level, as well as combining findings from multiple studies while maintaining track of false localization rates. We show that the approach is more effective than current processes that use a simpler mechanism for handling phosphosite identification redundancy within and across studies. In our case study using eight rice phosphoproteomics data sets, 6368 unique sites were confidently identified using our decoy approach compared to 4687 using traditional thresholding in which false localization rates are unknown.

Item Type:	Article
Uncontrolled Keywords:	proteomics, phosphorylation, post-translational-modification, false discovery rate, false localization rate, PTM, FDR, FLR, modification
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	05 Jun 2023 13:31
Last Modified:	29 Jun 2023 06:24
DOI:	10.1021/acs.jproteome.2c00823
Open Access URL:	https://doi.org/10.1021/acs.jproteome.2c00823
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3170831