Reusing Peptide Spectral Reference Libraries to Discover Putative Plasma Biomarkers of Response to Cancer Chemotherapy.

Matthew B O'Rourke, Philip P Hansbro, Mark P Molloy

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Matthew B O'RourkeBowel Cancer & Biomarker Laboratory, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, St Leonards, NSW, Australia.

Philip P HansbroCentre for Inflammation, Centenary Institute, Camperdown, NSW, Australia.

Mark P MolloyBowel Cancer & Biomarker Laboratory, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, St Leonards, NSW, Australia. m.molloy@sydney.edu.au.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Biofluids such as blood plasma are rich reservoirs of potential biomarkers for disease diagnosis, prognosis, and prediction of treatment response. However, mass spectrometry analysis of circulating plasma proteins remains challenging. The introduction of data-independent acquisition mass spectrometry (DIA-MS) is an important step toward addressing detection of less abundant plasma proteins. Numerous plasma peptide MS/MS spectral library datasets produced from extensive plasma fractionation are accessible from public archives, and these can be repurposed as spectral reference libraries to increase the depth of proteomic analysis when DIA-MS is used. Here we describe the workflow that relies on reusing the existing spectral reference libraries by populating them with locally obtained peptide MS/MS data acquired by DIA-MS. This approach was demonstrated effectively to identify putative plasma biomarkers of response to neoadjuvant chemotherapy in the setting of pancreatic ductal adenocarcinoma (PDAC) (O'Rourke et al., J Proteomics 231:103998, 2021).

Indexed as

Biomarkers, TumorPancreatic NeoplasmsProteomicsTandem Mass SpectrometryBlood ProteinsCarcinoma, Pancreatic DuctalHumansNeoadjuvant TherapyPeptide LibraryBiomarkers, TumorBlood ProteinsPeptide LibraryBiomarkerData-independent acquisitionMass spectrometryNeoadjuvant chemotherapyProteomics

Identifiers

PMID39052224

DOI10.1021/acs.jproteome.9b00090

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.