A proteomics sample metadata representation for multiomics integration and big data analysis.
Chengxin DaiAnja FüllgrabeJulianus PfeufferElizaveta M SolovyevaJingwen DengPablo MorenoSelvakumar KamatchinathanDeepti Jaiswal KunduNancy GeorgeSilvie FexovaBjoern Andreas GrueningMelanie Christine FöllJohannes GrissMarc VaudelEnrique AudainMarie Locard-PauletMichael TurewiczMartin EisenacherJulian UszkoreitTim Van Den BosscheVeit SchwämmleHenry WebelStefan SchulzeDavid BouyssiéSavita JayaramVinay Kumar DuggineniPatroklos SamarasMathias WilhelmMeena ChoiMingxun WangOliver KohlbacherAlvis BrazmaIrene PapatheodorouNuno BandeiraEric W DeutschJuan Antonio VizcainoMingze BaiTimo SachsenbergLev I LevitskyYasset Perez RiverolPublished in: Nature communications (2021)
The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.