Dataset Information

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.

ABSTRACT: The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ?20?000 human proteins encoded by the human genome.

SUBMITTER: Deutsch EW

PROVIDER: S-EPMC6986310 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.

Deutsch Eric W EW Lane Lydie L Overall Christopher M CM Bandeira Nuno N Baker Mark S MS Pineau Charles C Moritz Robert L RL Corrales Fernando F Orchard Sandra S Van Eyk Jennifer E JE Paik Young-Ki YK Weintraub Susan T ST Vandenbrouck Yves Y Omenn Gilbert S GS

Journal of proteome research 20191021 12

The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guid ...[more]

PMID: 31599596

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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 3.0.

Publications

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.

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