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Mass Spectrometry of Proteins pp 217–235Cite as

Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1977))

Abstract

Mass spectrometry based proteomics is no longer only a qualitative discipline, and can be successfully employed to obtain a truly multidimensional view of the proteome. In particular, systematic protein expression profiling is now a routine part of many studies in the field and beyond. The large growth in the number of quantitative studies is accompanied by a trend to share publicly the associated analysis results and the underlying raw data. This trend, established and strongly supported by public repositories such as the PRIDE database at the European Bioinformatics Institute, opens up enormous possibilities to explore the data beyond the original publications, for instance by reusing, reanalyzing, and performing different flavors of meta-analysis studies. To help researchers and scientists realize about this potential, here we describe the mainstream public proteomics resources containing quantitative proteomics data, including the processed analysis results and/or the underlying raw data. We then present and discuss the most important points to consider when attempting to (re)use proteomics data in the public domain. We conclude by highlighting potential pitfalls of (re)using quantitative data and discuss some of our own experiences in this context.

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Abbreviations

CPTAC:

Clinical Proteomic Tumor Analysis Consortium

DDA:

Data-dependent acquisition

DIA:

Data-independent acquisition

iTRAQ:

Isobaric tags for relative and absolute quantification

MIAME:

Minimum information about a microarray experiment

MIAPE:

Minimum information about a proteomics experiment

MRM:

Multiple reaction monitoring

MS:

Mass spectrometry

PRM:

Parallel reaction monitoring

PSM:

Peptide spectrum match

PTM:

Posttranslational modification

PX:

ProteomeXchange

SILAC:

Stable isotope labeling by amino acids in cell culture

TMT:

Tandem mass tag

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Acknowledgements

The authors want to acknowledge financial support from the Wellcome Trust [grant numbers WT101477MA and 208391/Z/17/Z] and from EMBL core funds.

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Authors and Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK

    Andrew F. Jarnuczak, Tobias Ternent & Juan Antonio Vizcaíno

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  1. Andrew F. Jarnuczak
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  2. Tobias Ternent
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  3. Juan Antonio Vizcaíno
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Correspondence to Juan Antonio Vizcaíno .

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Editors and Affiliations

  1. Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, South Yorkshire, UK

    Caroline A. Evans

  2. Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, UK

    Phillip C. Wright

  3. Laboratoire GBCM (EA4627), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France

    Josselin Noirel

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Jarnuczak, A.F., Ternent, T., Vizcaíno, J.A. (2019). Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities. In: Evans, C., Wright, P., Noirel, J. (eds) Mass Spectrometry of Proteins. Methods in Molecular Biology, vol 1977. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9232-4_14

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