Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

Eric W. Deutsch, Christopher M. Overall, Jennifer E. Van Eyk, Mark S. Baker, Young Ki Paik, Susan E Weintraub, Lydie Lane, Lennart Martens, Yves Vandenbrouck, Ulrike Kusebauch, William S. Hancock, Henning Hermjakob, Ruedi Aebersold, Robert L. Moritz, Gilbert S. Omenn

Research output: Contribution to journalReview article

77 Citations (Scopus)

Abstract

Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guidelines that should be applied to all HPP data contributions. For submission of manuscripts reporting HPP protein identification results, the guidelines are presented as a one-page checklist containing 15 essential points followed by two pages of expanded description of each. Here we present an overview of the guidelines and provide an in-depth description of each of the 15 elements to facilitate understanding of the intentions and rationale behind the guidelines, for both authors and reviewers. Broadly, these guidelines provide specific directions regarding how HPP data are to be submitted to mass spectrometry data repositories, how error analysis should be presented, and how detection of novel proteins should be supported with additional confirmatory evidence. These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.

Original languageEnglish (US)
Pages (from-to)3961-3970
Number of pages10
JournalJournal of Proteome Research
Volume15
Issue number11
DOIs
StatePublished - Nov 4 2016

Fingerprint

Proteome
Mass spectrometry
Mass Spectrometry
Guidelines
Manuscripts
Error analysis
Checklist
Proteins
Referral and Consultation
Research

Keywords

  • alternative protein matches
  • false-discovery rates
  • guidelines
  • Human Proteome Project
  • mass spectrometry
  • standards

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry

Cite this

Deutsch, E. W., Overall, C. M., Van Eyk, J. E., Baker, M. S., Paik, Y. K., Weintraub, S. E., ... Omenn, G. S. (2016). Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. Journal of Proteome Research, 15(11), 3961-3970. https://doi.org/10.1021/acs.jproteome.6b00392

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. / Deutsch, Eric W.; Overall, Christopher M.; Van Eyk, Jennifer E.; Baker, Mark S.; Paik, Young Ki; Weintraub, Susan E; Lane, Lydie; Martens, Lennart; Vandenbrouck, Yves; Kusebauch, Ulrike; Hancock, William S.; Hermjakob, Henning; Aebersold, Ruedi; Moritz, Robert L.; Omenn, Gilbert S.

In: Journal of Proteome Research, Vol. 15, No. 11, 04.11.2016, p. 3961-3970.

Research output: Contribution to journalReview article

Deutsch, EW, Overall, CM, Van Eyk, JE, Baker, MS, Paik, YK, Weintraub, SE, Lane, L, Martens, L, Vandenbrouck, Y, Kusebauch, U, Hancock, WS, Hermjakob, H, Aebersold, R, Moritz, RL & Omenn, GS 2016, 'Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1', Journal of Proteome Research, vol. 15, no. 11, pp. 3961-3970. https://doi.org/10.1021/acs.jproteome.6b00392
Deutsch, Eric W. ; Overall, Christopher M. ; Van Eyk, Jennifer E. ; Baker, Mark S. ; Paik, Young Ki ; Weintraub, Susan E ; Lane, Lydie ; Martens, Lennart ; Vandenbrouck, Yves ; Kusebauch, Ulrike ; Hancock, William S. ; Hermjakob, Henning ; Aebersold, Ruedi ; Moritz, Robert L. ; Omenn, Gilbert S. / Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. In: Journal of Proteome Research. 2016 ; Vol. 15, No. 11. pp. 3961-3970.
@article{cc64208b1ffb4eceb4771b4552103165,
title = "Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1",
abstract = "Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guidelines that should be applied to all HPP data contributions. For submission of manuscripts reporting HPP protein identification results, the guidelines are presented as a one-page checklist containing 15 essential points followed by two pages of expanded description of each. Here we present an overview of the guidelines and provide an in-depth description of each of the 15 elements to facilitate understanding of the intentions and rationale behind the guidelines, for both authors and reviewers. Broadly, these guidelines provide specific directions regarding how HPP data are to be submitted to mass spectrometry data repositories, how error analysis should be presented, and how detection of novel proteins should be supported with additional confirmatory evidence. These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.",
keywords = "alternative protein matches, false-discovery rates, guidelines, Human Proteome Project, mass spectrometry, standards",
author = "Deutsch, {Eric W.} and Overall, {Christopher M.} and {Van Eyk}, {Jennifer E.} and Baker, {Mark S.} and Paik, {Young Ki} and Weintraub, {Susan E} and Lydie Lane and Lennart Martens and Yves Vandenbrouck and Ulrike Kusebauch and Hancock, {William S.} and Henning Hermjakob and Ruedi Aebersold and Moritz, {Robert L.} and Omenn, {Gilbert S.}",
year = "2016",
month = "11",
day = "4",
doi = "10.1021/acs.jproteome.6b00392",
language = "English (US)",
volume = "15",
pages = "3961--3970",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "11",

}

TY - JOUR

T1 - Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

AU - Deutsch, Eric W.

AU - Overall, Christopher M.

AU - Van Eyk, Jennifer E.

AU - Baker, Mark S.

AU - Paik, Young Ki

AU - Weintraub, Susan E

AU - Lane, Lydie

AU - Martens, Lennart

AU - Vandenbrouck, Yves

AU - Kusebauch, Ulrike

AU - Hancock, William S.

AU - Hermjakob, Henning

AU - Aebersold, Ruedi

AU - Moritz, Robert L.

AU - Omenn, Gilbert S.

PY - 2016/11/4

Y1 - 2016/11/4

N2 - Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guidelines that should be applied to all HPP data contributions. For submission of manuscripts reporting HPP protein identification results, the guidelines are presented as a one-page checklist containing 15 essential points followed by two pages of expanded description of each. Here we present an overview of the guidelines and provide an in-depth description of each of the 15 elements to facilitate understanding of the intentions and rationale behind the guidelines, for both authors and reviewers. Broadly, these guidelines provide specific directions regarding how HPP data are to be submitted to mass spectrometry data repositories, how error analysis should be presented, and how detection of novel proteins should be supported with additional confirmatory evidence. These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.

AB - Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guidelines that should be applied to all HPP data contributions. For submission of manuscripts reporting HPP protein identification results, the guidelines are presented as a one-page checklist containing 15 essential points followed by two pages of expanded description of each. Here we present an overview of the guidelines and provide an in-depth description of each of the 15 elements to facilitate understanding of the intentions and rationale behind the guidelines, for both authors and reviewers. Broadly, these guidelines provide specific directions regarding how HPP data are to be submitted to mass spectrometry data repositories, how error analysis should be presented, and how detection of novel proteins should be supported with additional confirmatory evidence. These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.

KW - alternative protein matches

KW - false-discovery rates

KW - guidelines

KW - Human Proteome Project

KW - mass spectrometry

KW - standards

UR - http://www.scopus.com/inward/record.url?scp=84994589431&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84994589431&partnerID=8YFLogxK

U2 - 10.1021/acs.jproteome.6b00392

DO - 10.1021/acs.jproteome.6b00392

M3 - Review article

VL - 15

SP - 3961

EP - 3970

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 11

ER -