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Determining the full complement of protein-coding genes is a key goal ofgenome annotation. The most powerful approach for confirming protein codingpotential is the detection of cellular protein expression through peptide massspectrometry experiments. Here we map the peptides detected in 7 large-scaleproteomics studies to almost 60% of the protein coding genes in the GENCODEannotation the human genome. We find that conservation across vertebratespecies and the age of the gene family are key indicators of whether a peptidewill be detected in proteomics experiments. We find peptides for most highlyconserved genes and for practically all genes that evolved before bilateria. Atthe same time there is almost no evidence of protein expression for genes thathave appeared since primates, or for genes that do not have any protein-likefeatures or cross-species conservation. We identify 19 non-protein-likefeatures such as weak conservation, no protein features or ambiguousannotations in major databases that are indicators of low peptide detectionrates. We use these features to describe a set of 2,001 genes that arepotentially non-coding, and show that many of these genes behave more likenon-coding genes than protein-coding genes. We detect peptides for just 3% ofthese genes. We suggest that many of these 2,001 genes do not code for proteinsunder normal circumstances and that they should not be included in the humanprotein coding gene catalogue. These potential non-coding genes will be revisedas part of the ongoing human genome annotation effort.

The shrinking human protein coding complement: are there now fewer than 20,000 genes?