Guidelines for reporting quantitative mass spectrometry based experiments in proteomics

February 3, 2015

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Publicated to: Journal Of Proteomics. 95 (95): 84-88 - 2013-12-16 95(95), DOI: 10.1016/j.jprot.2013.02.026

Authors:

Martinez-Bartolome, Salvador; Deutsch, Eric W; Binz, Pierre-Alain; Jones, Andrew R; Eisenacher, Martin; Mayer, Gerhard; Campos, Alex; Canals, Francesc; Bech-Serra, Joan-Josep; Carrascal, Montserrat; Gay, Marina; Paradela, Alberto; Navajas, Rosana; Marcilla, Miguel; Luisa Hernaez, Maria; Dolores Gutierrez-Blazquez, Maria; Clemente Velarde, Luis Felipe; Aloria, Kerman; Beaskoetxea, Jabier; Alberto Medina-Aunon, J; Albar, Juan P

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Affiliations

CSIC, Ctr Nacl Biotecnol, Prote Facil, ProteoRed ISCIII, Madrid 28049, Spain - Author

Inst Syst Biol, Seattle, WA 98103 USA - Author

ProteoRed ISCIII, Barcelona, Spain - Author

Ruhr Univ Bochum, Med Proteom Ctr, Bochum, Germany - Author

Swiss Inst Bioinformat, CH-1211 Geneva 4, Switzerland - Author

UAB, CSIC,ProteoRed ISCIII, Inst Invest Biomed August Pi & Sunyer IIBB, Inst Invest Biomed Barcelona,IDIBAPS,Prote Lab, Bellaterra, Spain - Author

Univ Basque Country, Dept Biochem & Mol Biol, UPV EHU, ProteoRed ISCIII, Leioa 48940, Spain - Author

Univ Basque Country, UPV EHU, ProteoRed ISCHI, Prote Core Facil SGIKER, Leioa 48940, Spain - Author

Univ Complutense Madrid, Prote Unit, ProteoRed ISCIII, Madrid, Spain - Author

Univ Liverpool, Inst Integrat Biol, Liverpool L69 3BX, Merseyside, England - Author

Vall dHebron Univ Hosp, Vall dHebron Inst Oncol, ProteoRed ISCIII, Prote Lab, Barcelona, Spain - Author

Abstract

Mass spectrometry is already a well-established protein identification tool and recent methodological and technological developments have also made possible the extraction of quantitative data of protein abundance in large-scale studies. Several strategies for absolute and relative quantitative proteomics and the statistical assessment of quantifications are possible, each having specific measurements and therefore, different data analysis workflows. The guidelines for Mass Spectrometry Quantification allow the description of a wide range of quantitative approaches, including labeled and label-free techniques and also targeted approaches such as Selected Reaction Monitoring (SRM).The HUPO Proteomics Standards Initiative (HUPO-PSI) has invested considerable efforts to improve the standardization of proteomics data handling, representation and sharing through the development of data standards, reporting guidelines, controlled vocabularies and tooling. In this manuscript, we describe a key output from the HUPO-PSI-namely the MIAPE Quant guidelines, which have developed in parallel with the corresponding data exchange format mzQuantML [1]. The MIAPE Quant guidelines describe the HUPO-PSI proposal concerning the minimum information to be reported when a quantitative data set, derived from mass spectrometry (MS), is submitted to a database or as supplementary information to a journal. The guidelines have been developed with input from a broad spectrum of stakeholders in the proteomics field to represent a true consensus view of the most important data types and metadata, required for a quantitative experiment to be analyzed critically or a data analysis pipeline to be reproduced. It is anticipated that they will influence or be directly adopted as part of journal guidelines for publication and by public proteomics databases and thus may have an impact on proteomics laboratories across the world. This article is part of a Special Issue entitled: Standardization and Quality Control.Copyright © 2013 Elsevier B.V. All rights reserved.

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Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Journal of Proteomics due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2013, it was in position 16/78, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemical Research Methods.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-25:

Open Alex: 50
WoS: 35
Scopus: 37
Europe PMC: 25

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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Amsterdam; Germany; Switzerland; United Kingdom; United States of America.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Martinez Florensa, Mario) .

the author responsible for correspondence tasks has been Martinez Florensa, Mario.

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