The growing need for controlled data access models in clinical proteomics and metabolomics

Keane, Thomas M.; O′Donovan, Claire; Vizcaíno, Juan Antonio

doi:10.1038/s41467-021-26110-4

Cited by 20 publications

(16 citation statements)

References 12 publications

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“…At present, all data in PRIDE (and in all PX resources) is fully open. Therefore, there is an increasing number of clinical sensitive human datasets that cannot be made available via PRIDE due to ethical-related issues ( 55 ). To address this problem, we will be working in developing a tailored infrastructure for sensitive human proteomics data, and in all the related policies.…”

Section: Discussion and Future Plansmentioning

confidence: 99%

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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4,449

2,678

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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: Discussion and Future Plansmentioning

confidence: 99%

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

4,449

2,678

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“…Multi‐omics has been used in various studies to integrate data from different omics approaches [41–43]. The combination of proteomic and metabolomic analyses of the same sample is of high interest [44]. In 2020, Zougman et al.…”

Section: Modification Of Suspension Trapping Digestion Methodsmentioning

confidence: 99%

“…Multi-omics has been used in various studies to integrate data from different omics approaches [41][42][43]. The combination of proteomic and metabolomic analyses of the same sample is of high interest [44]. In 2020, Zougman et al reported a simultaneous trapping (Si-Trap) method to integrate proteomics and metabolomics in the same sample extract [38].…”

Section: Simultaneous Trappingmentioning

confidence: 99%

A review of suspension trapping digestion method in bottom‐up proteomics

Duong

Park

Lee

2022

J of Separation Science

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The standard bottom‐up proteomic workflow is comprised of sample preparation, data acquisition, and data analysis. While the latter two parts have made considerable advances in the last decade, sample preparation has remained an important challenge within the workflow due to the multi‐step nature of complex biological samples, and still requires much development. Several sample preparation methods have been developed and used in the last two decades, including in‐gel, in‐solution, on‐bead, filter‐aided sample preparation, and suspension trapping, to improve reproducibility, efficiency, scalability, and reduce the handling time of this process. One of the most recent methods developed and applied in proteomics studies in recent years is suspension trapping, which combines rapid detergent removal, reactor‐type protein digestion, and peptide clean‐up in a tip or spin column. Suspension trapping is a simple, rapid, and reproducible digestion method that can effectively handle proteins in low microgram or sub‐microgram amounts. This review discusses the benefits of the suspension trapping digestion method in relation to its development and application in bottom‐up proteomics studies. We also discuss recent applications of suspension trapping digestion to different sample types and the features of the suspension trapping digestion method compared with other sample preparation methods.

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“…The discussion about whether human sensitive proteomics data should be subjected to the same access restrictions as sensitive DNA/RNA sequencing data has just started. 74,75 The PSI will then follow closely the developments of the GA4GH since clearly, some existing standards could be adapted or extended to support proteomics data, if needed. In our view, definitely, it would not make sense to "reinvent the wheel".…”

Section: Future Work and Synergies With Other Organizationsmentioning

confidence: 99%

The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

Deutsch

Vizcaíno²,

Jones

et al. 2022

Preprint

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The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception twenty years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.

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The growing need for controlled data access models in clinical proteomics and metabolomics

Cited by 20 publications

References 12 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

A review of suspension trapping digestion method in bottom‐up proteomics

The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

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