Dataset Information

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.

SUBMITTER: Deutsch EW

PROVIDER: S-EPMC5096969 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

Deutsch Eric W EW Overall Christopher M CM Van Eyk Jennifer E JE Baker Mark S MS Paik Young-Ki YK Weintraub Susan T ST Lane Lydie L Martens Lennart L Vandenbrouck Yves Y Kusebauch Ulrike U Hancock William S WS Hermjakob Henning H Aebersold Ruedi R Moritz Robert L RL Omenn Gilbert S GS

Journal of proteome research 20160824 11

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 a ...[more]

PMID: 27490519

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Project description:Background and objectiveGingival crevicular fluid has been of major interest for many decades as a valuable body fluid that may serve as a source of biomarkers for both periodontal and systemic diseases. Owing to its very small sample size, submicroliter volumes, identification of its protein composition by classical biochemical methods has been limited. The advent of highly sensitive mass spectrometric technology has permitted large-scale identification of protein components of many biological samples. This technology has been employed to identify the protein composition of gingival crevicular fluid from inflamed and periodontal sites. In this report, we present a proteome data set of gingival crevicular fluid from healthy periodontium sites.Material and methodsA combination of a periopaper collection method with application of multidimensional protein separation and mass spectrometric technology led to a large-scale documentation of the proteome of gingival crevicular fluid from healthy periodontium sites.ResultsThe approaches used have culminated in identification of 199 proteins in gingival crevicular fluid of periodontally healthy sites. The present gingival crevicular fluid proteome from healthy sites was compared and contrasted with those proteomes of gingival crevicular fluid from inflamed and periodontal sites, as well as serum. The cross-correlation of the gingival crevicular fluid and plasma proteomes permitted dissociation of the 199 identified gingival crevicular fluid proteins into 105 proteins (57%) that can be identified in plasma and 94 proteins (43%) that are distinct and unique to the gingival crevicular fluid microenvironment. Such analysis also revealed distinctions in protein functional categories between serum proteins and those specific to the gingival crevicular fluid microenvironment.ConclusionFirstly, the data presented herein provide the proteome of gingival crevicular fluid from periodontally healthy sites through establishment of innovative analytical approaches for effective analysis of gingival crevicular fluid from periopapers both at the level of complete elusion and with removal of abundant albumin, which restricts identification of low-abundant proteins. Secondly, it adds significantly to the knowledge of gingival crevicular fluid composition and highlights new groups of proteins specific to the gingival crevicular fluid microenvironment.

Dataset Information

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

Publications

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

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