Inverting proteomics analysis provides powerful insight into the peptide/protein conundrum

In proteomics, a large proportion of mass spectrometry (MS) data is ignored due to the lack of, or insufficient statistical evidence for mappable peptides. In reality, only a small fraction of features are expected to be differentially relevant anyway. Mapping spectra to peptides and subsequently, proteins, produces uncertainty at several levels. We propose it is better to analyze proteomic profiling data directly at MS level, and then relate these features to peptides/proteins. In a renal cancer data comprising 12 normal and 12 cancer subjects, we demonstrate that a simple rule-based binning approach can give rise to informative features. We note that the peptides associated with significant spectral bins gave rise to better class separation than the corresponding proteins, suggesting a loss of signal in the peptide-to-protein transition. Additionally, the binning approach sharpens focus on relevant protein splice forms rather than just canonical sequences. Taken together, the inverted raw spectra analysis paradigm, which is realised by the MZ-Bin method described in this article, provides new possibilities and insights, in how MS-data can be interpreted.