Enhanced missing proteins detection in NCI60 cell lines using an integrative search engine approach

45 p.-11 fig.-6 tab. Guruceaga, Elizabeth et al.The Human Proteome Project (HPP) aims deciphering the complete map of the human proteome. In the last few years significant efforts of the HPP teams have been dedicated to the experimental detection of the missing proteins, which lack reliable mass spectrometry evidences of their existence. In this endeavor, an in depth analysis of shotgun experiments might represent a valuable resource to select a biological matrix in which design validation experiments. In this work we used all the proteomic experiments from the NCI60 cell lines and applied an integrative approach based on the results obtained from Comet, Mascot, OMSSA and X!Tandem. This workflow benefits from the complementarity of these search engines to increase the proteome coverage. Five missing proteins C-HPP guidelines compliant were identified although further validation is needed. Moreover, 165 missing proteins were detected with only one unique peptide and their functional analysis supported their participation in cellular pathways as was also proposed in other studies. Finally, we performed a combined analysis of the gene expression levels and the proteomic identifications from the common cell lines between the NCI60 and the CCLE project to suggest alternatives for further validation of missing protein observations.This work was supported by: PRBB and the Carlos III National Health Institute Agree- ment, PRBB-ISCIII (PT13/0001/0002); grants SAF2014-5478-R from Ministerio de Ciencia e Innovaci ́on and ISCIII-RETIC RD06/0020 to FJC, grant BIO2015- 66489-R to JIC and grants 33/2015 from Dpto. de Salud of Gobierno de Navarra and DPI2015-68982-R from Ministerio de Ciencia e Innovación to VS. J.A.V. and Y.P.R. are supported by the Wellcom Trust [grant number WT101477MA].Peer reviewe