title: Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence.
abstract: The current catalogue of the human proteome is not yet complete, as experimental proteomics evidence is still elusive for a group of proteins known as the missing proteins. The Human Proteome Project (HPP) has been successfully using technology and bioinformatic resources to improve the characterization of such challenging proteins. In this manuscript, we propose a pipeline starting with the mining of the PRIDE database to select a group of data sets potentially enriched in missing proteins that are subsequently analyzed for protein identification with a method based on the statistical analysis of proteotypic peptides. Spermatozoa and the HEK293 cell line were found to be a promising source of missing proteins and clearly merit further attention in future studies. After the analysis of the selected samples, we found 342 PSMs, suggesting the presence of 97 missing proteins in human spermatozoa or the HEK293 cell line, while only 36 missing proteins were potentially detected in the retina, frontal cortex, aorta thoracica, or placenta. The functional analysis of the missing proteins detected confirmed their tissue specificity, and the validation of a selected set of peptides using targeted proteomics (SRM/MRM assays) further supports the utility of the proposed pipeline. As illustrative examples, DNAH3 and TEPP in spermatozoa, and UNCX and ATAD3C in HEK293 cells were some of the more robust and remarkable identifications in this study. We provide evidence indicating the relevance to carefully analyze the ever-increasing MS/MS data available from PRIDE and other repositories as sources for missing proteins detection in specific biological matrices as revealed for HEK293 cells.
authors: Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.
authors: Alba
authors: A
authors: Garin-Muga
authors: Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.|IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain.
authors: Leticia
authors: L
authors: Odriozola
authors: Proteomics Unit, Spanish National Cancer Research Centre , 28029, Madrid, Spain.
authors: Ana
authors: A
authors: Martínez-Val
authors: European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust GenomeCampus, Hinxton, Cambridge, CB10 1SD, U.K.
authors: Noemí
authors: N
authors: Del Toro
authors: Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.
authors: Rocío
authors: R
authors: Martínez
authors: Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.
authors: Manuela
authors: M
authors: Molina
authors: Proteomics Unit (SCSIE), University of Valencia , 46010, Valencia, Spain.
authors: Laura
authors: L
authors: Cantero
authors: Andrology Laboratory and Sperm Bank, Instituto Universitario IVI , 46015, Valencia, Spain.
authors: Rocío
authors: R
authors: Rivera
authors: Andrology Laboratory and Sperm Bank, Instituto Universitario IVI , 46015, Valencia, Spain.
authors: Nicolás
authors: N
authors: Garrido
authors: Fundación IVI/INCLIVA , 46010, Valencia, Spain.
authors: Francisco
authors: F
authors: Dominguez
authors: Biochemistry Department, University of Valencia , 46010, Valencia, Spain.
authors: Manuel M
authors: MM
authors: Sanchez Del Pino
authors: European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust GenomeCampus, Hinxton, Cambridge, CB10 1SD, U.K.
authors: Juan Antonio
authors: JA
authors: Vizcaíno
authors: Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.|IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain.|Division of Hepatology and Gene Therapy, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.
authors: Fernando J
authors: FJ
authors: Corrales
authors: Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.|IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain.
authors: Victor
authors: V
authors: Segura
mesh_terms: D001011:Aorta / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005260:Female; D005625:Frontal Lobe / Q000737:chemistry; D057809:HEK293 Cells; D006801:Humans; D008297:Male; D010920:Placenta / Q000737:chemistry; D011247:Pregnancy; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D012160:Retina / Q000737:chemistry; D013094:Spermatozoa / Q000737:chemistry; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome
keywords: C-HPP; MS/MS proteomics; PRIDE database; missing proteins