A Proteomics Sample Metadata Representation for Multiomics Integration and Big Data Analysis

The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.

Citing Articles

Temporal phosphoproteomics reveals circuitry of phased propagation in insulin signaling.

Turewicz M, Skagen C, Hartwig S, Majda S, Thedinga K, Herwig R Nat Commun. 2025; 16(1):1570.

PMID: 39939313 PMC: 11821911. DOI: 10.1038/s41467-025-56335-6.

Cooperation of GlycoPOST and UniCarb-DR towards a comprehensive glycomics data repository workflow.

Takahashi Y, Karlsson N, Okuda S, Aoki-Kinoshita K Anal Bioanal Chem. 2024; 417(5):1015-1023.

PMID: 39611991 PMC: 11782440. DOI: 10.1007/s00216-024-05673-3.

The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.

Klein J, Lam H, Mak T, Bittremieux W, Perez-Riverol Y, Gabriels R Anal Chem. 2024; 96(46):18491-18501.

PMID: 39514576 PMC: 11579979. DOI: 10.1021/acs.analchem.4c04091.

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.

Rajczewski A, Blakeley-Ruiz J, Meyer A, Vintila S, McIlvin M, Van Den Bossche T bioRxiv. 2024; .

PMID: 39345414 PMC: 11430069. DOI: 10.1101/2024.09.18.613707.

A roadmap to the molecular human linking multiomics with population traits and diabetes subtypes.

Halama A, Zaghlool S, Thareja G, Kader S, Al Muftah W, Mook-Kanamori M Nat Commun. 2024; 15(1):7111.

PMID: 39160153 PMC: 11333501. DOI: 10.1038/s41467-024-51134-x.

References

Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaino J . Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics. 2014; 15(5-6):930-49. PMC: 4409848. DOI: 10.1002/pmic.201400302. View

Sarkans U, Fullgrabe A, Ali A, Athar A, Behrangi E, Diaz N . From ArrayExpress to BioStudies. Nucleic Acids Res. 2020; 49(D1):D1502-D1506. PMC: 7778911. DOI: 10.1093/nar/gkaa1062. View

Pfeuffer J, Sachsenberg T, Alka O, Walzer M, Fillbrunn A, Nilse L . OpenMS - A platform for reproducible analysis of mass spectrometry data. J Biotechnol. 2017; 261:142-148. DOI: 10.1016/j.jbiotec.2017.05.016. View

Gonzalez-Beltran A, Maguire E, Sansone S, Rocca-Serra P . linkedISA: semantic representation of ISA-Tab experimental metadata. BMC Bioinformatics. 2014; 15 Suppl 14:S4. PMC: 4255742. DOI: 10.1186/1471-2105-15-S14-S4. View

Deutsch E, Orchard S, Binz P, Bittremieux W, Eisenacher M, Hermjakob H . Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J Proteome Res. 2017; 16(12):4288-4298. PMC: 5715286. DOI: 10.1021/acs.jproteome.7b00370. View

Maguire E, Gonzalez-Beltran A, Whetzel P, Sansone S, Rocca-Serra P . OntoMaton: a bioportal powered ontology widget for Google Spreadsheets. Bioinformatics. 2012; 29(4):525-7. PMC: 3570217. DOI: 10.1093/bioinformatics/bts718. View

Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D . BioSamples database: an updated sample metadata hub. Nucleic Acids Res. 2018; 47(D1):D1172-D1178. PMC: 6323949. DOI: 10.1093/nar/gky1061. View

Sinitcyn P, Tiwary S, Rudolph J, Gutenbrunner P, Wichmann C, Yilmaz S . MaxQuant goes Linux. Nat Methods. 2018; 15(6):401. DOI: 10.1038/s41592-018-0018-y. View

Bai J, Bandla C, Guo J, Vera Alvarez R, Bai M, Vizcaino J . BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers. J Proteome Res. 2021; 20(4):2056-2061. PMC: 7611561. DOI: 10.1021/acs.jproteome.0c00904. View

10.

Gruning B, Dale R, Sjodin A, Chapman B, Rowe J, Tomkins-Tinch C . Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018; 15(7):475-476. PMC: 11070151. DOI: 10.1038/s41592-018-0046-7. View

11.

Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N . Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010; 26(8):1112-8. PMC: 2853691. DOI: 10.1093/bioinformatics/btq099. View

12.

Choi M, Carver J, Chiva C, Tzouros M, Huang T, Tsai T . MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nat Methods. 2020; 17(10):981-984. PMC: 7541731. DOI: 10.1038/s41592-020-0955-0. View

13.

Fullgrabe A, George N, Green M, Nejad P, Aronow B, Fexova S . Guidelines for reporting single-cell RNA-seq experiments. Nat Biotechnol. 2020; 38(12):1384-1386. PMC: 9302581. DOI: 10.1038/s41587-020-00744-z. View

14.

Watanabe Y, Yoshizawa A, Ishihama Y, Okuda S . The jPOST Repository as a Public Data Repository for Shotgun Proteomics. Methods Mol Biol. 2021; 2259:309-322. DOI: 10.1007/978-1-0716-1178-4_20. View

15.

Jarmusch A, Wang M, Aceves C, Advani R, Aguirre S, Aksenov A . ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods. 2020; 17(9):901-904. PMC: 7968862. DOI: 10.1038/s41592-020-0916-7. View

16.

Mertins P, Mani D, Ruggles K, Gillette M, Clauser K, Wang P . Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016; 534(7605):55-62. PMC: 5102256. DOI: 10.1038/nature18003. View

17.

Ma J, Chen T, Wu S, Yang C, Bai M, Shu K . iProX: an integrated proteome resource. Nucleic Acids Res. 2018; 47(D1):D1211-D1217. PMC: 6323926. DOI: 10.1093/nar/gky869. View

18.

Choi M, Chang C, Clough T, Broudy D, Killeen T, MacLean B . MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics. 2014; 30(17):2524-6. DOI: 10.1093/bioinformatics/btu305. View

19.

Griss J, Jones A, Sachsenberg T, Walzer M, Gatto L, Hartler J . The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Proteomics. 2014; 13(10):2765-75. PMC: 4189001. DOI: 10.1074/mcp.O113.036681. View

20.

Athar A, Fullgrabe A, George N, Iqbal H, Huerta L, Ali A . ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2018; 47(D1):D711-D715. PMC: 6323929. DOI: 10.1093/nar/gky964. View