DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics

Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed sp...

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Autores principales: Midha, Mukul K., Campbell, David S., Kapil, Charu, Kusebauch, Ulrike, Hoopmann, Michael R., Bader, Samuel L., Moritz, Robert L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567827/
https://www.ncbi.nlm.nih.gov/pubmed/33067471
http://dx.doi.org/10.1038/s41467-020-18901-y
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author Midha, Mukul K.
Campbell, David S.
Kapil, Charu
Kusebauch, Ulrike
Hoopmann, Michael R.
Bader, Samuel L.
Moritz, Robert L.
author_facet Midha, Mukul K.
Campbell, David S.
Kapil, Charu
Kusebauch, Ulrike
Hoopmann, Michael R.
Bader, Samuel L.
Moritz, Robert L.
author_sort Midha, Mukul K.
collection PubMed
description Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide, the quality control of these libraries is lacking. We present the DIALib-QC (DIA library quality control) software tool for the systematic evaluation of a library’s characteristics, completeness and correctness across 62 parameters of compliance, and further provide the option to improve its quality. We demonstrate its utility in assessing and repairing spectral libraries for correctness, accuracy and sensitivity.
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spelling pubmed-75678272020-10-19 DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics Midha, Mukul K. Campbell, David S. Kapil, Charu Kusebauch, Ulrike Hoopmann, Michael R. Bader, Samuel L. Moritz, Robert L. Nat Commun Article Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide, the quality control of these libraries is lacking. We present the DIALib-QC (DIA library quality control) software tool for the systematic evaluation of a library’s characteristics, completeness and correctness across 62 parameters of compliance, and further provide the option to improve its quality. We demonstrate its utility in assessing and repairing spectral libraries for correctness, accuracy and sensitivity. Nature Publishing Group UK 2020-10-16 /pmc/articles/PMC7567827/ /pubmed/33067471 http://dx.doi.org/10.1038/s41467-020-18901-y Text en © The Author(s) 2020 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
Midha, Mukul K.
Campbell, David S.
Kapil, Charu
Kusebauch, Ulrike
Hoopmann, Michael R.
Bader, Samuel L.
Moritz, Robert L.
DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
title DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
title_full DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
title_fullStr DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
title_full_unstemmed DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
title_short DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
title_sort dialib-qc an assessment tool for spectral libraries in data-independent acquisition proteomics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567827/
https://www.ncbi.nlm.nih.gov/pubmed/33067471
http://dx.doi.org/10.1038/s41467-020-18901-y
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