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.

http://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkab1038/41031430/gkab1038.pdf

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

Background 
There is an increasing international interest in patient and public involvement (PPI) in research, yet relatively little robust evidence exists about its impact on health and social care research.
 
Objective
 
To identify the impact of patient and public involvement on health and social care research.
 
Design
 
A systematic search of electronic databases and health libraries was undertaken from 1995 to 2009. Data were extracted and quality assessed utilizing the guidelines of the NHS Centre for Reviews and Dissemination 2009 and the Critical Appraisal Skills Programme (CASP). Grey literature was assessed using the Dixon-Woods et al. (2005) checklist.
 
Inclusion criteria
 
All study types that reported the impact PPI had on the health and/or social care research study.
 
Main results
 
A total of 66 studies reporting the impact of PPI on health and social care research were included. The positive impacts identified enhanced the quality and appropriateness of research. Impacts were reported for all stages of research, including the development of user-focused research objectives, development of user-relevant research questions, development of user-friendly information, questionnaires and interview schedules, more appropriate recruitment strategies for studies, consumer-focused interpretation of data and enhanced implementation and dissemination of study results. Some challenging impacts were also identified.
 
Conclusion
 
This study provides the first international evidence of PPI impact that has emerged at all key stages of the research process. However, much of the evidence base concerning impact remains weak and needs significant enhancement in the next decade.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1369-7625.2012.00795.x

Mapping the impact of patient and public involvement on health and social care research: a systematic review

Objective
Patient and public involvement (PPI) in research has expanded nationally and internationally over the last decade, and recently there has been significant attention given to understanding its impact on research. Less attention has been given to the impact of PPI on the people involved, yet it has been shown that the success of PPI in research can be reliant on the processes of engagement between these individuals and communities. This paper therefore critically explores the impact of PPI on service users, researchers and communities involved in health and social care research.

https://www.researchgate.net/profile/Carole_Mockford/publication/264054422_A_Systematic_Review_of_the_Impact_of_Patient_and_Public_Involvement_on_Service_Users_Researchers_and_Communities/links/544111790cf2a6a049a4ca0b.pdf

A systematic review of the impact of patient and public involvement on service users, researchers and communities.

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.

/pdf/the-proteomexchange-consortium-at-10-years-2023-update-1avgkari.pdf

The ProteomeXchange consortium at 10 years: 2023 update

Public involvement at the design stage of primary health research : A narrative review of case examples

The policy imperative to increase public participation in health and social care research, planning and service delivery raises significant questions about optimum approaches, methods and the extent to which this policy can influence change in practice. This paper highlights the key policy literature on user involvement and participatory research methods to establish the context for a partnership research project exploring perceptions of risk in relation to falls from the perspectives of older people, carers, and health and social care professionals. The paper reports the methods used in developing user involvement in the research at a number of levels, including project management, and a consumer panel working alongside the research team and influencing the dissemination in local falls prevention strategies. The authors draw out the issues related to the context and method of involvement, and discuss the impact on research quality and local service development in health and social care.

Involving older people in research: methodological issues.

The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets. 

/pdf/implementing-the-reuse-of-public-dia-proteomics-datasets-354drpp7.pdf

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

1 Department of Computer Science, The University of Manchester, Manchester, United Kingdom, 2 Melandra Limited, Stockport, United Kingdom, 3 Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands, 4 Research IT, IT Services, University of Manchester, Manchester, United Kingdom, 5 Meise Botanic Garden, Meise, Belgium, 6 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium, 7 VIB Center for Plant Systems Biology, Ghent, Belgium, 8 Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany, 9 Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden

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Involving older people in research: methodological issues.

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

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