Cargando…

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic...

Descripción completa

Detalles Bibliográficos
Autores principales: Searle, Brian C., Pino, Lindsay K., Egertson, Jarrett D., Ting, Ying S., Lawrence, Robert T., MacLean, Brendan X., Villén, Judit, MacCoss, Michael J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277451/
https://www.ncbi.nlm.nih.gov/pubmed/30510204
http://dx.doi.org/10.1038/s41467-018-07454-w
_version_ 1783378154045308928
author Searle, Brian C.
Pino, Lindsay K.
Egertson, Jarrett D.
Ting, Ying S.
Lawrence, Robert T.
MacLean, Brendan X.
Villén, Judit
MacCoss, Michael J.
author_facet Searle, Brian C.
Pino, Lindsay K.
Egertson, Jarrett D.
Ting, Ying S.
Lawrence, Robert T.
MacLean, Brendan X.
Villén, Judit
MacCoss, Michael J.
author_sort Searle, Brian C.
collection PubMed
description Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment. These coordinates calibrate protein databases or spectrum libraries to a specific mass spectrometer and chromatography setup, facilitating DIA-only pipelines and the reuse of global resource libraries. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect 20–25% more peptides from DIA experiments than with data dependent acquisition-based spectrum libraries alone.
format Online
Article
Text
id pubmed-6277451
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-62774512018-12-05 Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry Searle, Brian C. Pino, Lindsay K. Egertson, Jarrett D. Ting, Ying S. Lawrence, Robert T. MacLean, Brendan X. Villén, Judit MacCoss, Michael J. Nat Commun Article Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment. These coordinates calibrate protein databases or spectrum libraries to a specific mass spectrometer and chromatography setup, facilitating DIA-only pipelines and the reuse of global resource libraries. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect 20–25% more peptides from DIA experiments than with data dependent acquisition-based spectrum libraries alone. Nature Publishing Group UK 2018-12-03 /pmc/articles/PMC6277451/ /pubmed/30510204 http://dx.doi.org/10.1038/s41467-018-07454-w Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Searle, Brian C.
Pino, Lindsay K.
Egertson, Jarrett D.
Ting, Ying S.
Lawrence, Robert T.
MacLean, Brendan X.
Villén, Judit
MacCoss, Michael J.
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
title Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
title_full Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
title_fullStr Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
title_full_unstemmed Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
title_short Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
title_sort chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277451/
https://www.ncbi.nlm.nih.gov/pubmed/30510204
http://dx.doi.org/10.1038/s41467-018-07454-w
work_keys_str_mv AT searlebrianc chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry
AT pinolindsayk chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry
AT egertsonjarrettd chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry
AT tingyings chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry
AT lawrencerobertt chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry
AT macleanbrendanx chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry
AT villenjudit chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry
AT maccossmichaelj chromatogramlibrariesimprovepeptidedetectionandquantificationbydataindependentacquisitionmassspectrometry