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Reporting guidelines for proteomics

The context-sensitive nature of transcriptome, metabolome and proteome data necessitates the capture of a richer set of metadata (data about the data) than is required for basic genetic sequence, where usually knowing the organism of origin will suffice. The use of paper citations as proxies for actual metadata hinders the reassessment of data sets, and obstructs non-standard searching (e.g. by the order that different liquid chromatography columns were coupled). The requirements of the various journals also differ, so important detail may be lacking in some cases, or presented in an esoteric fashion.

There is then a need for public repositories that contain information from whole proteomics experiments; making explicit both where samples came from, and how analyses of them were performed. It is therefore appropriate to attempt to define the minimum set of information about a proteomics experiment that would be required by such a repository.

Up-to-date released documents and working drafts

Acronym        TopicVersion  StatusComment
MIAPE MIAPE Principles document1.0release 
MIAPE-MSMass Spectrometry2.98releasereplaces v2.24
MIAPE-MSIMass Spectrometry Informatics1.1release 
MIAPE-QuantMass Spectrometry Quantification  1.0release 
MIAPE-GEGel Electrophoresis1.4release 
MIAPE-GIGel Informatics1release 
MIAPE-CCColumn Chromatography1.1release 
MIAPE-CECapillary Electrophoresis0.9.3release 
MIMIxMolecular Interactions1-1-2release 
     
More details and history of the documents are available from the MIAPE-docs page. 
 

Published components of MIAPE:

The 'MIAPE Principles' document:
The minimum information about a proteomics experiment (MIAPE), Nature Biotechnology 25, 887-893 (2007)
-- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Molecular Interactions experiments:
The minimum information required for reporting a molecular interaction experiment (MIMIx)
, Nature Biotechnology 25, 894-898 (2007) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Mass Spectrometry experiments:
Guidelines for reporting the use of mass spectrometry in proteomics, Nature Biotechnology 26, 860-861 (2008) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Mass Spectrometry Informatics experiments:
Guidelines for reporting the use of mass spectrometry informatics in proteomics, Nature Biotechnology 26, 862 (2008) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Gel Electrophoresis experiments:
Guidelines for reporting the use of gel electrophoresis in proteomics, Nature Biotechnology 26, 863 (2008) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Gel Informatics experiments:
Guidelines for reporting the use of gel image informatics in proteomics, Nature Biotechnology 28, 655-656 (2010) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Column Chromatography experiments:
Guidelines for reporting the use of column chromatography in proteomics, Nature Biotechnology 28, 654 (2010) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Capillary Electrophoresis experiments:
Guidelines for reporting the use of capillary electrophoresis in proteomics, Nature Biotechnology 28, 654-655 (2010) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. Journal of Proteomics 2013 Mar 14 -- DOI -- PubMed.

Up-to-date released documents and working drafts available from this site here

MIAPE is now registered with the MIBBI Project (Minimum Information for Biological and Biomedical Investigations), which promotes and coordinates the development and management of Minimum Information (MI) specifications from across the biological and biomedical sciences.

Implementers

ProteoRed: see bioinformatics team wiki page.