DART-ID increases single-cell proteome coverage

Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammali...

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Autores principales: Chen, Albert Tian, Franks, Alexander, Slavov, Nikolai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6625733/
https://www.ncbi.nlm.nih.gov/pubmed/31260443
http://dx.doi.org/10.1371/journal.pcbi.1007082
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author Chen, Albert Tian
Franks, Alexander
Slavov, Nikolai
author_facet Chen, Albert Tian
Franks, Alexander
Slavov, Nikolai
author_sort Chen, Albert Tian
collection PubMed
description Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30–50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net.
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spelling pubmed-66257332019-07-25 DART-ID increases single-cell proteome coverage Chen, Albert Tian Franks, Alexander Slavov, Nikolai PLoS Comput Biol Research Article Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30–50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net. Public Library of Science 2019-07-01 /pmc/articles/PMC6625733/ /pubmed/31260443 http://dx.doi.org/10.1371/journal.pcbi.1007082 Text en © 2019 Chen et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chen, Albert Tian
Franks, Alexander
Slavov, Nikolai
DART-ID increases single-cell proteome coverage
title DART-ID increases single-cell proteome coverage
title_full DART-ID increases single-cell proteome coverage
title_fullStr DART-ID increases single-cell proteome coverage
title_full_unstemmed DART-ID increases single-cell proteome coverage
title_short DART-ID increases single-cell proteome coverage
title_sort dart-id increases single-cell proteome coverage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6625733/
https://www.ncbi.nlm.nih.gov/pubmed/31260443
http://dx.doi.org/10.1371/journal.pcbi.1007082
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