PNNL

Abstract

The term proteoform, introduced in these pages in 20131, has rapidly gained acceptance in the proteomics community. The challenge and importance of comprehensively identifying proteoforms in complex samples has been recognized, and reports have begun to appear of new platforms towards that end2-5. However, one interesting central ambiguity has emerged, namely determining precisely what is meant by a “proteoform identification”. At present, the only practical approaches for establishing the exact primary structure of a proteoform employ mass spectrometry (MS), and there is a wide range of MS results that provide “proteoform identifications6”. This seemingly small matter has significant impact, as the ambiguity in knowing what is meant by an “identification” makes it difficult to compare results from different laboratories and approaches. This situation hinders the ability of the community to evaluate technological progress and to efficiently expand biological knowledge. To address this issue, we propose a five-level system for classifying proteoform identifications. The classification scheme stems directly from a consideration of the four types of possible ambiguity possible for a proteoform identification, ranging from the most subtle (i.e., precise localization of a post-translational modification, or PTM) to the most dramatic (i.e., ambiguity in the gene of origin). The five classes then correspond to the level of ambiguity present in the identification, ranging from no ambiguity at all (Level 1), to ambiguity of all four types (Level 5). Details of the scheme are provided in Table 1 and Supplementary Table 1, with specific use cases and examples provided in Supplementary Figure 1.