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Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry
Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisit...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The American Society for Biochemistry and Molecular Biology
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442367/ https://www.ncbi.nlm.nih.gov/pubmed/30651306 http://dx.doi.org/10.1074/mcp.TIR118.001276 |
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author | Müller, Fränze Kolbowski, Lars Bernhardt, Oliver M. Reiter, Lukas Rappsilber, Juri |
author_facet | Müller, Fränze Kolbowski, Lars Bernhardt, Oliver M. Reiter, Lukas Rappsilber, Juri |
author_sort | Müller, Fränze |
collection | PubMed |
description | Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS(3)) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 10%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favorably to DDA where we quantified cross-links across triplicates with a CV of 66%, for a single protein. We found DIA-QCLMS to be capable of detecting changing abundances of cross-linked peptides in complex mixtures, despite the ratio compression encountered when increasing sample complexity through the addition of E. coli cell lysate as matrix. In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS. |
format | Online Article Text |
id | pubmed-6442367 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | The American Society for Biochemistry and Molecular Biology |
record_format | MEDLINE/PubMed |
spelling | pubmed-64423672019-04-02 Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry Müller, Fränze Kolbowski, Lars Bernhardt, Oliver M. Reiter, Lukas Rappsilber, Juri Mol Cell Proteomics Technological Innovation and Resources Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS(3)) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 10%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favorably to DDA where we quantified cross-links across triplicates with a CV of 66%, for a single protein. We found DIA-QCLMS to be capable of detecting changing abundances of cross-linked peptides in complex mixtures, despite the ratio compression encountered when increasing sample complexity through the addition of E. coli cell lysate as matrix. In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS. The American Society for Biochemistry and Molecular Biology 2019-04 2019-01-16 /pmc/articles/PMC6442367/ /pubmed/30651306 http://dx.doi.org/10.1074/mcp.TIR118.001276 Text en © 2019 Müller et al. Published by The American Society for Biochemistry and Molecular Biology, Inc. Author's Choice—Final version open access under the terms of the Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0) . |
spellingShingle | Technological Innovation and Resources Müller, Fränze Kolbowski, Lars Bernhardt, Oliver M. Reiter, Lukas Rappsilber, Juri Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry |
title | Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry |
title_full | Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry |
title_fullStr | Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry |
title_full_unstemmed | Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry |
title_short | Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry |
title_sort | data-independent acquisition improves quantitative cross-linking mass spectrometry |
topic | Technological Innovation and Resources |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442367/ https://www.ncbi.nlm.nih.gov/pubmed/30651306 http://dx.doi.org/10.1074/mcp.TIR118.001276 |
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