MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets

Meena Choi; Jeremy Carver; Cristina Chiva; Manuel Tzouros; Ting Huang; Tsung-Heng Tsai; Benjamin Pullman; Oliver M Bernhardt; Ruth Hüttenhain; Guo Ci Teo; Yasset Perez-Riverol; Jan Muntel; Maik Müller; Sandra Goetze; Maria Pavlou; Erik Verschueren; Bernd Wollscheid; Alexey I Nesvizhskii; Lukas Reiter; Tom Dunkley; Eduard Sabidó; Nuno Bandeira; Olga Vitek

doi:10.1038/s41592-020-0955-0

MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets

Nat Methods. 2020 Oct;17(10):981-984. doi: 10.1038/s41592-020-0955-0. Epub 2020 Sep 14.

Authors

Meena Choi¹, Jeremy Carver², Cristina Chiva^{3

4}, Manuel Tzouros⁵, Ting Huang¹, Tsung-Heng Tsai¹, Benjamin Pullman², Oliver M Bernhardt⁶, Ruth Hüttenhain⁷, Guo Ci Teo⁸, Yasset Perez-Riverol⁹, Jan Muntel⁶, Maik Müller¹⁰, Sandra Goetze^{10

11}, Maria Pavlou¹⁰, Erik Verschueren⁷, Bernd Wollscheid^{10

11}, Alexey I Nesvizhskii⁸, Lukas Reiter⁶, Tom Dunkley⁵, Eduard Sabidó^{3

4}, Nuno Bandeira¹², Olga Vitek¹³

Affiliations

¹ Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
² Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
³ Proteomics Unit, Center for Genomics Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
⁴ Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain.
⁵ Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland.
⁶ Biognosys, Zurich, Switzerland.
⁷ Department of Molecular and Cellular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
⁸ Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
⁹ Proteomics Services, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
¹⁰ Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland.
¹¹ Swiss Institute of Bioinformatics, Lausanne, Switzerland.
¹² Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. bandeira@ucsd.edu.
¹³ Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA. o.vitek@northeastern.edu.

Abstract

MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry-based proteomics, which is compatible with all mass spectrometry data acquisition types and computational analysis tools. A branch structure enables MassIVE.quant to systematically store raw experimental data, metadata of the experimental design, scripts of the quantitative analysis workflow, intermediate input and output files, as well as alternative reanalyses of the same dataset.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Databases, Protein*
Fungal Proteins / chemistry
Mass Spectrometry*
Proteomics*
Reproducibility of Results
Saccharomyces cerevisiae / metabolism
Software

Substances

Fungal Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding