Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach

The Human Proteome
Project (HPP) aims deciphering the complete
map of the human proteome. In the past few years, significant efforts
of the HPP teams have been dedicated to the experimental detection
of the missing proteins, which lack reliable mass spectrometry evidence
of their existence. In this endeavor, an in depth analysis of shotgun
experiments might represent a valuable resource to select a biological
matrix in 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.