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The spHPP MRM-DB: A database to support MRM assays

The spHPP MRM-DB: A database to support MRM assays. Vital Vialas Fernandez – Bioinformatics WorkingGroup @ UCM La Cristalera – Miraflores – 11/12/12. Introduction. … previously on Miraflores… Lack of consensus on how to report SRM assays results by the different labs:

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The spHPP MRM-DB: A database to support MRM assays

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  1. ThespHPP MRM-DB: A databasetosupport MRM assays Vital VialasFernandez – BioinformaticsWorkingGroup @ UCM La Cristalera – Miraflores – 11/12/12

  2. Introduction …previouslyon Miraflores… Lack of consensus on how to report SRM assays results by the different labs: - When is a peptide considered proteotypic? - Peptide identity validated with msms full scan? - How many transitions need to be reported? - etc,... Creation of spreadsheet template to be filled by labs La Cristalera – Miraflores – 11/12/12

  3. Spreadsheettemplateforreporting MRM results proteins La Cristalera – Miraflores – 11/12/12

  4. Spreadsheettemplateforreporting MRM results peptides La Cristalera – Miraflores – 11/12/12

  5. Definitions: Assayed, Observed, Validated, Verified • Proteotypicpeptide: unambiguouslyprotein/isoformidentifier. • Assayedpeptides: Number of assayedpeptideswhetherobservedornot • Observedpeptides: Number of peptidesforwith 2 or more coelutingtransitions • Verifiedpeptides: Identifiedby IDA (Qtrap MSMS) or >3 coelutingtransitionsmatchingobserved MSMS spectrum (shotgun/targetedanalysis) • Validatedpeptides: Peptidesverifiedby at least 3 differentlabs La Cristalera – Miraflores – 11/12/12

  6. Spreadsheettemplateforreporting MRM results transitions La Cristalera – Miraflores – 11/12/12

  7. MRM workgroupspreadsheets “external” resources server @ UCM La Cristalera – Miraflores – 11/12/12

  8. Bioinformaticsworkinggroup. Tasks • Create a database to store and access all these data (spreadsheets) generated in the MRM experiments • Accommodate assayed transitions and all related parameters for detecting one particular protein in a MRM experiment • Framework to check multi-centric validation of MRM methods keeping track of the source, i.e. instrument, set up, cell line, etc.. • Multiplatform Java GUI (A.Medina) for queries and showing the data La Cristalera – Miraflores – 11/12/12

  9. What you get: (that you can't with spreadsheets) • Simultaneous accessibility by many users to the same data (spreadsheets are not meant to be updated by more than one person at a time) • Possibility of creating different roles for accessing or storing/updating data • Efficiency. Up to millions of records • Flexibility in retrieval of data through more or less complex queries • Enforces referential integrity of the data. I.e. keep track of all related data La Cristalera – Miraflores – 11/12/12

  10. Use Cases Isthispeptideproteotypic? Has anyotherlabtriedtodetectthispeptide? What transitions have they found? Wasitvalidatedwith full MS/MS fragmentation? Whichcell line, instrument, column, gradientwereused? Is there a method to detect a particular protein that is validated by at least 3 different labs? La Cristalera – Miraflores – 11/12/12

  11. GUI basada en Java (multiplataforma) con conexión a la BD MySqlrealizada a través de la interface Hybernate. El usuarioinicia la búsqueda a partir de un Gene ID (ensembl) Todaslasproteínasasociadas a ese GEN se carganaquí. Selecionandouna y pinchando en Search, se cargan los péptidos (proteotípicosasociados y paracadauno de estos sus fragmentos (Q1 + Q3). β A.Medina

  12. El sistema, además de proporcionar la información (atributos) contenidos en lastablas, informasi la entradaestá o no revisadaporSwissProt (isoforma “preferida” u otra) El usuariopuedecomprobarsilastransicionesque ha detectadocorresponden o no con lasincluidad en la BD, inicialmenteextraidas de la informacióndisponible en MRMAtlas. β A.Medina

  13. EL sp-HPP en la UCM Concha Gil WG 1.- ProteinExpression: MªL Hernáez, Elvira Marín, Felipe Clemente WG 2.- SRM: MªLHernáez, David Cáceres, Felipe Clemente WG 4.- Bioinformatics: Vital Vialas WG 5.- ClinicalHealthCare & Biobanking: Lucía Monteoliva, Aida Pitarch, Elvira Marín La Cristalera – Miraflores – 11/12/12

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