Universal Spectrum Identifier for mass spectra

Deutsch, Eric W.; Perez‐Riverol, Yasset; Carver, Jeremy; Kawano, Shin; Mendoza, Luis; Bossche, Tim Van Den; Gabriels, Ralf; Binz, Pierre‐Alain; Pullman, Benjamin; Sun, Zhi; Shofstahl, Jim; Bittremieux, Wout; Mak, Tytus D.; Klein, Joshua; Zhu, Yunping; Lam, Henry H N; Vizcaíno, Juan Antonio; Bandeira, Nuno

doi:10.1038/s41592-021-01184-6

Cited by 56 publications

(53 citation statements)

References 20 publications

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“…The public availability and direct access to mass spectra data create the opportunity for scientists to directly assess whether, e.g., a novel peptide evidence, PTM, or amino acid variant (SAAV) are supported by a good-quality and well-annotated mass spectrum ( 19 , 37 ). PSI and PX partners have recently created a novel mechanism to uniquely resolve each mass spectrum in public proteomics resources.…”

Section: Current Status Of the Pride Ecosystem: Resources And Toolsmentioning

confidence: 99%

“…PSI and PX partners have recently created a novel mechanism to uniquely resolve each mass spectrum in public proteomics resources. The Universal Spectrum Identifier (USI) enables greater transparency of spectral evidence making it more ‘FAIR’ (Findable, Accessible, Interoperable, and Reusable), with more than 1 billion USI identifications from over 3 billion spectra already available through PX repositories ( 19 ).…”

Section: Current Status Of the Pride Ecosystem: Resources And Toolsmentioning

confidence: 99%

“…As of 2021, the resources PeptideAtlas ( 13 ), including its related resource PASSEL (PeptideAtlas SRM Experiment Library) ( 14 ), MassIVE ( 15 ), jPOST ( 16 ), iProX ( 17 ) and Panorama Public ( 18 ) are the active members of the consortium. PX coordinates the release of accession numbers for every submitted dataset and a set of services for providing unified access to publicly available datasets ( http://proteomecentral.proteomexchange.org/cgi/GetDataset ), including specific data types such as mass spectra, using Universal Spectrum Identifiers ( 19 ) ( http://proteomecentral.proteomexchange.org/usi/ ). Additionally, in 2017, PRIDE became an ELIXIR ( http://www.elixir-europe.org ) core data resource ( 20 ) and ELIXIR deposition database, recognizing its key role in the life sciences.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez‐Riverol

Bai

Bandla

et al. 2021

Nucleic Acids Research

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3,241

1,841

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The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.

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Section: Current Status Of the Pride Ecosystem: Resources And Toolsmentioning

confidence: 99%

Section: Current Status Of the Pride Ecosystem: Resources And Toolsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez‐Riverol

Bai

Bandla

et al. 2021

Nucleic Acids Research

Self Cite

3,241

1,841

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“…The ability to refer to specific spectra of high importance and cite data in published manuscripts was done by implementing a new standardized Universal Spectrum Identifier (USI) proposed by PX ( 14 , 15 ). The USI is a multi-part key separated by colon characters; for example, mzspec:PXD006512:CNHPP_HCC_LC_profiling_L006_P_F1:scan:64442:VADALTNAVAHVDDMPNALSALSDLHAHK/3.…”

Section: Universal Spectrum Identifier (Usi)mentioning

confidence: 99%

iProX in 2021: connecting proteomics data sharing with big data

Chen

Liu

et al. 2021

Nucleic Acids Research

Self Cite

237

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The rapid development of proteomics studies has resulted in large volumes of experimental data. The emergence of big data platform provides the opportunity to handle these large amounts of data. The integrated proteome resource, iProX (https://www.iprox.cn), which was initiated in 2017, has been greatly improved with an up-to-date big data platform implemented in 2021. Here, we describe the main iProX developments since its first publication in Nucleic Acids Research in 2019. First, a hyper-converged architecture with high scalability supports the submission process. A hadoop cluster can store large amounts of proteomics datasets, and a distributed, RESTful-styled Elastic Search engine can query millions of records within one second. Also, several new features, including the Universal Spectrum Identifier (USI) mechanism proposed by ProteomeXchange, RESTful Web Service API, and a high-efficiency reanalysis pipeline, have been added to iProX for better open data sharing. By the end of August 2021, 1526 datasets had been submitted to iProX, reaching a total data volume of 92.42TB. With the implementation of the big data platform, iProX can support PB-level data storage, hundreds of billions of spectra records, and second-level latency service capabilities that meet the requirements of the fast growing field of proteomics.

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“…Until this is done, we will be unable to advance our methods or thus deep and routine proteomic analyses to the extent that is both necessary and sufficient for unbiased identification of genuine highly selective biomarkers and drug targets. That said, there are indeed critical ongoing efforts to improve both sample and data analyses, and the best of these must be integrated into a continuously developing unified approach to proteoform and thus proteome analysis [29,81,88,[257][258][259][260][261][262][263][264][265][266][267][268][269][270][271][272][273][274]. We are hopeful and confident of a more collaborative and unbiased future for the discipline of proteomics.…”

Section: What Next?mentioning

confidence: 99%

Proteomes Are of Proteoforms: Embracing the Complexity

2021

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Proteomes are complex—much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current ‘state-of-the-field’. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?

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Universal Spectrum Identifier for mass spectra

Cited by 56 publications

References 20 publications

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

iProX in 2021: connecting proteomics data sharing with big data

Proteomes Are of Proteoforms: Embracing the Complexity

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