cHPP chomosome 2 and 14 : a joint initiative between France and Switzerland Lydie Lane, HUPO 2013, Yokohama

Toulouse Grenoble Strasbourg Proteomics French Infrastructure 3 Proteomic Platforms Task Force : 15 MS instruments / ~100 people CALIPHO group, Geneva

Current actions: In addition to integrating all HPP-relevant datasets into neXtProt, we specifically : 1- re-annotate all proteins from chromosomes 2 and 14 based on literature (in collaboration with UniProtKB/Swiss-Prot) 2- try to identify missing proteins from chromosomes 2 and 14 using existing (unpublished) MS datasets

Reannotation of 20 «missing» chr. 2 proteins Integration of PeptideAtlas builds + 6 other datasets Missing proteins (neXtProt release Sept 2013): 210 (chr. 2) 123 (chr. 14)

Identifying missing proteins from chromosomes 2 and 14 using existing datasets Chrom peptides bank -351 entries non validated at protein level according to neXtProt, (release aug 2013) -> theoretical peptides unique, tryptic/semi tryptic *.dat ProFI *.dat files 67 entries 29 entries Mascot score >30 PepLength >6 E-value <=0.05 Manual spectra inspection 8 newly identified proteins (6 on chr 2, 2 on chr 14)

6 newly identified proteins on chr transmembrane proteins found in «membrane ghosts» fractions from different cell lines - KCNS3 (1 peptide) -TMEM169 (1 peptide) - LINC00116 (1 peptide) - TEX261 (1 peptide found in various samples : hepatocarcinoma, neural stem cells, U87 cells (glioblastoma cell line), and TG01/TG16/TG10 (primary glioblastoma cells) - 1 protein identified in urine : KLHL30 (1 peptide) - 1 protein identified in U937 cells (monocytic cell line) : POTEKP (2 peptides) Ion score Mascot: 69,3 m/z=618,41 LGILVVFSFIK -> These identifications need to be validated by dedicated SRM and Ab-based studies

2 newly identified proteins on chr putative membrane-associated protein found in «membrane ghosts» from primary neural stem cells : MDGA2 (4 peptides with high quality spectra) 1 protein identified in urine : KLHL30 (1 peptide) -1 protein identified in blood platelets : DHRS4L1 (1 peptide) Ion score Mascot: 50,2 Evalue Omssa : 6,8 m/z=813,40 PTM: propionamide (C) FTDFGTYTCVASLK

Perspectives : How to improve the coverage? -Increase the number of processed *.dat files (56’138 new files are being processed) -Adapt the workflow in order to take the ~850’000 cSNPs annotated in neXtProt into account

Acknowledgements: Lydie Lane (chrom. 2 PI, CALIPHO, SIB, Geneva, CH) Amos Bairoch (CALIPHO, SIB, Geneva, CH) Alain Gateau (CALIPHO, SIB, Geneva, CH) Paula Duek (CALIPHO, SIB, Geneva, CH) Lionel Breuza (Swiss-Prot, SIB, Geneva, CH) Sylvain Poux (Swiss-Prot, SIB, Geneva, CH) Jérome Garin (chrom. 14 PI, ProFI's coord., CEA, Grenoble, FR) Yves Vandenbrouck (Bioinformatics coord., CEA, Grenoble, FR) Christophe Bruley (CEA, Grenoble, FR) Alexandre Burel (CNRS, Strasbourg, FR) Christine Carapito (CNRS, Strasbourg, FR) Alain Van Dorsselaer (CNRS, Strasbourg, FR) David Bouyssié (CNRS, Toulouse, FR) Anne Gonzales de Peredo (CNRS, Toulouse, FR) Odile Schiltz-Burlet (CNRS, Toulouse, FR) Jacques Haiech (Faculté de Pharmacie, Strasbourg, FR) Hervé Chneiweiss (Hôpital Saint Anne, Paris, FR) Jamila Faivre (Hôpital Paul Brousse, Villejuif, FR)