The ProteomeXchange consortium at 10 years: 2023 update

Abstract

Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.

Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite

“…Although the TPP does not use the Proteomics Standards Initiative − (PSI) standard format mzIdentML internally, the final output of a TPP analysis may be exported to mzIdentML 1.2 via the TPP tool tpp2mzid for deposition to ProteomeXchange − repositories or for use with other mzIdentML-supporting tools. In the other direction, users may use the ProteoWizard idconvert tool (bundled with TPP) to convert externally acquired mzIdentML files to pepXML for further TPP processing.…”

Interpreting biologically informed neural networks for enhanced biomarker discovery and pathway analysis

“…Blood-plasma from patients suffering from septic AKI and COVID-19 were gathered and analyzed elsewhere, whereafter the resulting proteomic datasets were uploaded to proteomeXchange [46] and made publicly available [47,29]. The COVID-19 dataset consisting of the raw data matrix of quantified precursors and design matrix with patient annotations were downloaded from PRIDE (PXD025752) [48] and re-analyzed.…”

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

“…Central to storing the raw data behind cryo-EM experiments, EMPIAR also archives volume EM and X-ray tomography images and provides visualisation tools for them. Further popular databases reporting updates this year include the Chemical Probes Portal ( 96 ) which has quintupled in size since first publication, and ProteomeXchange ( 97 ), the consortium of high-throughput proteomics resources, which celebrates 10 years. Finally, LitCovid reports an update ( 98 ) on its efforts to capture and curate the literature on COVID-19 with new emphasis on long COVID-19, variants and vaccines; while the collection of 3000 culture media for 40 000 microbial strains at Media Dive ( 99 ) will undoubtedly prove invaluable for microbiologists.…”