Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

Abstract

Remarkable progress continues on the annotation of the proteins identified in the Human Proteome and on finding credible proteomic evidence for the expression of “missing proteins”. Missing proteins are those with no previous protein-level evidence or insufficient evidence to make a confident identification upon reanalysis in PeptideAtlas and curation in neXtProt. Enhanced with several major new data sets published in 2014, the human proteome presented as neXtProt, version 2014-09-19, has 16 491 unique confident proteins (PE level 1), up from 13 664 at 2012-12 and 15 646 at 2013-09. That leaves 2948 missing proteins from genes classified having protein existence level PE 2, 3, or 4, as well as 616 dubious proteins at PE 5. Here, we document the progress of the HPP and discuss the importance of assessing the quality of evidence, confirming automated findings and considering alternative protein matches for spectra and peptides. We provide guidelines for proteomics investigators to apply in reporting newly identified proteins.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics

“…Figure 9 presented a drawback for parsimonious approaches that reported more single peptide proteins compared with probabilistic models such as Fido and ProteinLP. The "two peptides"-rule, applied quite often in proteomics to control protein false discoveries (46), can affect and change the results of the experiment depending of the inference algorithm used.…”

“…In fact, it is more relevant to see whether the true protein groups are reported. There are several publicly available datasets containing ground truth data for peptides (46) and only relatively small protein datasets (47). Only the yeast dataset used can be considered as a complex mixture.…”

“…As a further quality assessment metric for reliable identifications, we analyzed the number of peptides per protein groups for each protein inference algorithm (46). The numbers of peptides per protein group were plotted in a heatmap-like way for the results of the PXD000603 dataset with the Swiss-Prot database ( Figure 9).…”

From proteomics to personalized medicine: the road ahead

“…Under the guidance of the Human Proteome Organisation (HUPO) over 80% of the proteins predicted by the human genome have now been identified using either mass spectrometric or antibody-based techniques, and the remaining 'missing proteins' are being steadily accounted for [6,7]. Resources such as the Human MRM Atlas, a comprehensive resource designed to enable scientists to perform quantitative analysis of all human proteins, are being developed to facilitate reproducible transfer of quantitative assays between laboratories.…”

Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status

“…In the latest neXtProt release (2016-01-11), there are 2949 PE2-4 proteins out of a total of 20055 entries. One of the first aims of the C-HPP teams is to confidently detect these so-called "missing proteins" using mass spectrometry (MS) and antibodybased techniques 3 . Currently, a protein is considered validated by MS when two unique, non-nested peptides of at least 9 amino acids (aa) have been identified in human biological samples (www.thehpp.org/guidelines; Deutsch et al, 2016, submitted).…”