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Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses

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Standard

Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses. / Sørensen, Lars; Salbo, Rune.

In: Journal of The American Society for Mass Spectrometry, Vol. 29, No. 11, 11.2018, p. 2278-2281.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Sørensen, L & Salbo, R 2018, 'Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses', Journal of The American Society for Mass Spectrometry, vol. 29, no. 11, pp. 2278-2281. https://doi.org/10.1007/s13361-018-2056-1

APA

Sørensen, L., & Salbo, R. (2018). Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses. Journal of The American Society for Mass Spectrometry, 29(11), 2278-2281. https://doi.org/10.1007/s13361-018-2056-1

CBE

Sørensen L, Salbo R. 2018. Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses. Journal of The American Society for Mass Spectrometry. 29(11):2278-2281. https://doi.org/10.1007/s13361-018-2056-1

MLA

Sørensen, Lars and Rune Salbo. "Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses". Journal of The American Society for Mass Spectrometry. 2018, 29(11). 2278-2281. https://doi.org/10.1007/s13361-018-2056-1

Vancouver

Sørensen L, Salbo R. Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses. Journal of The American Society for Mass Spectrometry. 2018 Nov;29(11):2278-2281. https://doi.org/10.1007/s13361-018-2056-1

Author

Sørensen, Lars ; Salbo, Rune. / Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses. In: Journal of The American Society for Mass Spectrometry. 2018 ; Vol. 29, No. 11. pp. 2278-2281.

Bibtex

@article{07d9206d60f7490c8406ba62c8ed0ccb,
title = "Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses",
abstract = "Hydrogen deuterium exchange measured by mass spectrometry (HDX-MS) is a commonly used technique for studying the structural dynamics of proteins in solution. The first part of any bottom-up HDX-MS experiment is to identify the peptides generated from a digestion step. This requires manual inspection of the identified peptides to determine their use for HDX-MS analysis, which is a time-consuming task. Throughout the literature, there have been different approaches for removing peptides that do not yield quantifiable HDX information. This includes using validity scores from the software used in the generation of the peptide map and that the peptide should be found in two out of three technical replicate experiments. Here, we analyze the previously available methods for filtering the identified peptides in regard to their ability to predict whether a peptide will provide quantifiable HDX-MS data or not. We also present a new score-based system relying on a combination of MS/MS parameters that offers an improved method for separating quantifiable peptides from the nonquantifiable. Using this score-based method reduces the number of peptide spectra that needs to be manually inspected and thereby the time spent curating HDX-MS data. [Figure not available: see fulltext.]",
keywords = "Data analysis, HDX-MS, Peptide picking",
author = "Lars S{\o}rensen and Rune Salbo",
year = "2018",
month = nov,
doi = "10.1007/s13361-018-2056-1",
language = "English",
volume = "29",
pages = "2278--2281",
journal = "Journal of The American Society for Mass Spectrometry",
issn = "1044-0305",
publisher = "Springer Nature",
number = "11",

}

RIS

TY - JOUR

T1 - Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses

AU - Sørensen, Lars

AU - Salbo, Rune

PY - 2018/11

Y1 - 2018/11

N2 - Hydrogen deuterium exchange measured by mass spectrometry (HDX-MS) is a commonly used technique for studying the structural dynamics of proteins in solution. The first part of any bottom-up HDX-MS experiment is to identify the peptides generated from a digestion step. This requires manual inspection of the identified peptides to determine their use for HDX-MS analysis, which is a time-consuming task. Throughout the literature, there have been different approaches for removing peptides that do not yield quantifiable HDX information. This includes using validity scores from the software used in the generation of the peptide map and that the peptide should be found in two out of three technical replicate experiments. Here, we analyze the previously available methods for filtering the identified peptides in regard to their ability to predict whether a peptide will provide quantifiable HDX-MS data or not. We also present a new score-based system relying on a combination of MS/MS parameters that offers an improved method for separating quantifiable peptides from the nonquantifiable. Using this score-based method reduces the number of peptide spectra that needs to be manually inspected and thereby the time spent curating HDX-MS data. [Figure not available: see fulltext.]

AB - Hydrogen deuterium exchange measured by mass spectrometry (HDX-MS) is a commonly used technique for studying the structural dynamics of proteins in solution. The first part of any bottom-up HDX-MS experiment is to identify the peptides generated from a digestion step. This requires manual inspection of the identified peptides to determine their use for HDX-MS analysis, which is a time-consuming task. Throughout the literature, there have been different approaches for removing peptides that do not yield quantifiable HDX information. This includes using validity scores from the software used in the generation of the peptide map and that the peptide should be found in two out of three technical replicate experiments. Here, we analyze the previously available methods for filtering the identified peptides in regard to their ability to predict whether a peptide will provide quantifiable HDX-MS data or not. We also present a new score-based system relying on a combination of MS/MS parameters that offers an improved method for separating quantifiable peptides from the nonquantifiable. Using this score-based method reduces the number of peptide spectra that needs to be manually inspected and thereby the time spent curating HDX-MS data. [Figure not available: see fulltext.]

KW - Data analysis

KW - HDX-MS

KW - Peptide picking

UR - http://www.scopus.com/inward/record.url?scp=85054897489&partnerID=8YFLogxK

U2 - 10.1007/s13361-018-2056-1

DO - 10.1007/s13361-018-2056-1

M3 - Journal article

C2 - 30171440

AN - SCOPUS:85054897489

VL - 29

SP - 2278

EP - 2281

JO - Journal of The American Society for Mass Spectrometry

JF - Journal of The American Society for Mass Spectrometry

SN - 1044-0305

IS - 11

ER -