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

Walzer, Mathias; García-Seisdedos, David; Prakash, Ananth; Brack, Paul; Crowther, Peter; Rl, Graham; George, Nancy; Mohammed, Suhaib; Moreno, Pablo; Papatheodorou, Irene; Hubbard, Simon J.; Vizcaíno, Juan Antonio

doi:10.1101/2021.06.08.447493

Cited by 7 publications

(10 citation statements)

References 52 publications

(37 reference statements)

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“…After filtering out the disease and statistically insignificant pathways, there were 2,990 pathways found in all the organs of mouse and 2,162 pathways in all the organs of rat. In mouse samples, the largest number of pathways (367) were found in articular cartilage, and the lowest number of pathways was from liver (44). We also observed that Neuronal Systemrelated pathways are predominantly present in the brain and eye, which is consistent with expectations.…”

Section: Pathway Enrichment Analysissupporting

confidence: 90%

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Wang

García-Seisdedos

Prakash

et al. 2021

Preprint

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The increasingly large amount of public proteomics data enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contains 23 individual datasets, which have a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We compared protein expression between the different organs, including the distribution of proteins across them. We also performed gene ontology and pathway enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples. Finally, it should be noted that protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.

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Section: Pathway Enrichment Analysissupporting

confidence: 90%

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Wang

García-Seisdedos

Prakash

et al. 2021

Preprint

Self Cite

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“…Additionally, ten SWATH-MS DIA datasets coming mainly from cell line and human tumor samples have also already been re-analysed and integrated into Expression Atlas. In this case, an in-house open analysis pipeline based on OpenSWATH ( https://github.com/PRIDE-reanalysis/DIA-reanalysis ) was developed and used for the re-analysis ( 53 ). These datasets constituted a pilot project to study the feasibility of performing a systematic reanalysis and integration of DIA datasets.…”

Section: Pride Archive As a Hub Of Ms Evidencesmentioning

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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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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“…In this case, an in-house analysis pipeline was built using OpenSWATH as the base ( https://github.com/PRIDE-reanalysis/DIA-reanalysis ). These datasets constituted a pilot project to study the feasibility of performing a systematic reanalysis of DIA datasets and included cell-line, human cancer-related and plasma samples ( 27 ).…”

Section: Datasets and Speciesmentioning

confidence: 99%

Expression Atlas update: gene and protein expression in multiple species

Moreno

Fexová

George

et al. 2021

Nucleic Acids Research

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119

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The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from >4500 expression studies from >65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools. Each study's metadata are annotated using ontologies. The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas. Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to Single Cell RNA-Sequencing (scRNA-Seq) studies. The resource has been in continuous development since 2009 and it is available at https://www.ebi.ac.uk/gxa.

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

Cited by 7 publications

References 52 publications

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

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

Expression Atlas update: gene and protein expression in multiple species

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