The spHPP MRM-DB: A database to support MRM assays Vital Vialas Fernandez – Bioinformatics 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: - 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

proteins Spreadsheet template for reporting MRM results La Cristalera – Miraflores – 11/12/12

Spreadsheet template for reporting MRM results peptides La Cristalera – Miraflores – 11/12/12

 Proteotypic peptide: unambiguously protein/isoform identifier.  Assayed peptides: Number of assayed peptides whether observed or not  Observed peptides: Number of peptides for with 2 or more coeluting transitions  Verified peptides: Identified by IDA (Qtrap MSMS) or >3 coeluting transitions matching observed MSMS spectrum (shotgun/targeted analysis)  Validated peptides: Peptides verified by at least 3 different labs Definitions: Assayed, Observed, Validated, Verified La Cristalera – Miraflores – 11/12/12

Spreadsheet template for reporting MRM results transitions La Cristalera – Miraflores – 11/12/12

UCM MRM workgroup spreadsheets La Cristalera – Miraflores – 11/12/12 “external” resources

Bioinformatics working group. 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

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

Use Cases La Cristalera – Miraflores – 11/12/12 What transitions have they found? Which cell line, instrument, column, gradient were used? Has any other lab tried to detect this peptide? Is this peptide proteotypic? Was it validated with full MS/MS fragmentation? Is there a method to detect a particular protein that is validated by at least 3 different labs?

A.Medina GUI basada en Java (multiplataforma) con conexión a la BD MySql realizada a través de la interface Hybernate. El usuario inicia la búsqueda a partir de un Gene ID (ensembl) Todas las proteínas asociadas a ese GEN se cargan aquí. Selecionando una y pinchando en Search, se cargan los péptidos (proteotípicos asociados y para cada uno de estos sus fragmentos (Q1 + Q3). β

El sistema, además de proporcionar la información (atributos) contenidos en las tablas, informa si la entrada está o no revisada por SwissProt (isoforma “preferida” u otra) El usuario puede comprobar si las transiciones que ha detectado corresponden o no con las incluidad en la BD, inicialmente extraidas de la información disponible en MRMAtlas. A.Medina β

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