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Human proteome project mass spectrometry data interpretation guidelines 2.1

(2016) JOURNAL OF PROTEOME RESEARCH. 15(11). p.3961-3970
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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
guidelines, standards, Human Proteome Project, mass spectrometry, false-discovery rates, alternative protein matches, DECOY SEARCH STRATEGY, STATISTICAL-MODEL, MISSING PROTEINS, PRIDE DATABASE, IDENTIFICATIONS, CONFIDENCE, ACCURACY, LEUCINE, UPDATE, TOOLS

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Citation

Please use this url to cite or link to this publication:

MLA
Deutsch, Eric W et al. “Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.” JOURNAL OF PROTEOME RESEARCH 2016 : 3961–3970. Print.
APA
Deutsch, E. W., Overall, C. M., Van Eyk, J. E., Baker, M. S., Paik, Y.-K., Weintraub, S. T., Lane, L., et al. (2016). Human proteome project mass spectrometry data interpretation guidelines 2.1. JOURNAL OF PROTEOME RESEARCH.
Chicago author-date
Deutsch, Eric W, Christopher M Overall, Jennifer E Van Eyk, Mark S Baker, Young-Ki Paik, Susan T Weintraub, Lydie Lane, et al. 2016. “Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.” Journal of Proteome Research.
Chicago author-date (all authors)
Deutsch, Eric W, Christopher M Overall, Jennifer E Van Eyk, Mark S Baker, Young-Ki Paik, Susan T Weintraub, Lydie Lane, Lennart Martens, Yves Vandenbrouck, Ulrike Kusebauch, William S Hancock, Henning Hermjakob, Ruedi Aebersold, Robert L Moritz, and Gilbert S Omenn. 2016. “Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.” Journal of Proteome Research.
Vancouver
1.
Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik Y-K, Weintraub ST, et al. Human proteome project mass spectrometry data interpretation guidelines 2.1. JOURNAL OF PROTEOME RESEARCH. 2016. p. 3961–70.
IEEE
[1]
E. W. Deutsch et al., “Human proteome project mass spectrometry data interpretation guidelines 2.1,” JOURNAL OF PROTEOME RESEARCH, vol. 15, no. 11. pp. 3961–3970, 2016.
@misc{8524770,
  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.},
  author       = {Deutsch, Eric W and Overall, Christopher M and Van Eyk, Jennifer E and Baker, Mark S and Paik, Young-Ki and Weintraub, Susan T and Lane, Lydie and Martens, Lennart and Vandenbrouck, Yves and Kusebauch, Ulrike and Hancock, William S and Hermjakob, Henning and Aebersold, Ruedi and Moritz, Robert L and Omenn, Gilbert S},
  issn         = {1535-3893},
  keywords     = {guidelines,standards,Human Proteome Project,mass spectrometry,false-discovery rates,alternative protein matches,DECOY SEARCH STRATEGY,STATISTICAL-MODEL,MISSING PROTEINS,PRIDE DATABASE,IDENTIFICATIONS,CONFIDENCE,ACCURACY,LEUCINE,UPDATE,TOOLS},
  language     = {eng},
  number       = {11},
  pages        = {3961--3970},
  series       = {JOURNAL OF PROTEOME RESEARCH},
  title        = {Human proteome project mass spectrometry data interpretation guidelines 2.1},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.6b00392},
  volume       = {15},
  year         = {2016},
}

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