A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification

Prostate cancer is the most frequent form of cancer in men, accounting for more than one-third of all cases. Current screening techniques, such as PSA testing used in conjunction with routine procedures, lead to unnecessary biopsies and the discovery of low-risk tumours, resulting in overdiagnosis....

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Autores principales:	Ammara Muazzam, Davide Chiasserini, Janet Kelsall, Nophar Geifman, Anthony D. Whetton, Paul A. Townsend
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	prostate cancer spectral library blood proteomics protein peptide mass spectrometry Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
Acceso en línea:	https://doaj.org/article/babdd99ac9414efb8dac8193ca384248
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spelling	oai:doaj.org-article:babdd99ac9414efb8dac8193ca3842482021-11-11T15:35:53ZA Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification10.3390/cancers132155802072-6694https://doaj.org/article/babdd99ac9414efb8dac8193ca3842482021-11-01T00:00:00Zhttps://www.mdpi.com/2072-6694/13/21/5580https://doaj.org/toc/2072-6694Prostate cancer is the most frequent form of cancer in men, accounting for more than one-third of all cases. Current screening techniques, such as PSA testing used in conjunction with routine procedures, lead to unnecessary biopsies and the discovery of low-risk tumours, resulting in overdiagnosis. SWATH-MS is a well-established data-independent (DI) method requiring prior knowledge of targeted peptides to obtain valuable information from SWATH maps. In response to the growing need to identify and characterise protein biomarkers for prostate cancer, this study explored a spectrum source for targeted proteome analysis of blood samples. We created a comprehensive prostate cancer serum spectral library by combining data-dependent acquisition (DDA) MS raw files from 504 patients with low, intermediate, or high-grade prostate cancer and healthy controls, as well as 304 prostate cancer-related protein in silico assays. The spectral library contains 114,684 transitions, which equates to 18,479 peptides translated into 1227 proteins. The robustness and accuracy of the spectral library were assessed to boost confidence in the identification and quantification of prostate cancer-related proteins across an independent cohort, resulting in the identification of 404 proteins. This unique database can facilitate researchers to investigate prostate cancer protein biomarkers in blood samples. In the real-world use of the spectrum library for biomarker detection, using a signature of 17 proteins, a clear distinction between the validation cohort’s pre- and post-treatment groups was observed. Data are available via ProteomeXchange with identifier PXD028651.Ammara MuazzamDavide ChiasseriniJanet KelsallNophar GeifmanAnthony D. WhettonPaul A. TownsendMDPI AGarticleprostate cancerspectral libraryblood proteomicsproteinpeptidemass spectrometryNeoplasms. Tumors. Oncology. Including cancer and carcinogensRC254-282ENCancers, Vol 13, Iss 5580, p 5580 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	prostate cancer spectral library blood proteomics protein peptide mass spectrometry Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
spellingShingle	prostate cancer spectral library blood proteomics protein peptide mass spectrometry Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 Ammara Muazzam Davide Chiasserini Janet Kelsall Nophar Geifman Anthony D. Whetton Paul A. Townsend A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification
description	Prostate cancer is the most frequent form of cancer in men, accounting for more than one-third of all cases. Current screening techniques, such as PSA testing used in conjunction with routine procedures, lead to unnecessary biopsies and the discovery of low-risk tumours, resulting in overdiagnosis. SWATH-MS is a well-established data-independent (DI) method requiring prior knowledge of targeted peptides to obtain valuable information from SWATH maps. In response to the growing need to identify and characterise protein biomarkers for prostate cancer, this study explored a spectrum source for targeted proteome analysis of blood samples. We created a comprehensive prostate cancer serum spectral library by combining data-dependent acquisition (DDA) MS raw files from 504 patients with low, intermediate, or high-grade prostate cancer and healthy controls, as well as 304 prostate cancer-related protein in silico assays. The spectral library contains 114,684 transitions, which equates to 18,479 peptides translated into 1227 proteins. The robustness and accuracy of the spectral library were assessed to boost confidence in the identification and quantification of prostate cancer-related proteins across an independent cohort, resulting in the identification of 404 proteins. This unique database can facilitate researchers to investigate prostate cancer protein biomarkers in blood samples. In the real-world use of the spectrum library for biomarker detection, using a signature of 17 proteins, a clear distinction between the validation cohort’s pre- and post-treatment groups was observed. Data are available via ProteomeXchange with identifier PXD028651.
format	article
author	Ammara Muazzam Davide Chiasserini Janet Kelsall Nophar Geifman Anthony D. Whetton Paul A. Townsend
author_facet	Ammara Muazzam Davide Chiasserini Janet Kelsall Nophar Geifman Anthony D. Whetton Paul A. Townsend
author_sort	Ammara Muazzam
title	A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification
title_short	A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification
title_full	A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification
title_fullStr	A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification
title_full_unstemmed	A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification
title_sort	prostate cancer proteomics database for swath-ms based protein quantification
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/babdd99ac9414efb8dac8193ca384248
work_keys_str_mv	AT ammaramuazzam aprostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT davidechiasserini aprostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT janetkelsall aprostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT nophargeifman aprostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT anthonydwhetton aprostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT paulatownsend aprostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT ammaramuazzam prostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT davidechiasserini prostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT janetkelsall prostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT nophargeifman prostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT anthonydwhetton prostatecancerproteomicsdatabaseforswathmsbasedproteinquantification AT paulatownsend prostatecancerproteomicsdatabaseforswathmsbasedproteinquantification
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A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification

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