Figure 2.

Decision tree to guide the identification and characterization of unknown proteoforms, including those harboring multiple post-translational modifications or non-covalent cofactors. The name of select software tools used at each step are in italics, with an expanded list of common open-source and commercial resources detailed in Table S1. Much of this decision tree has been incorporated into a new nTDMS resource, ProSight Native, that provides a platform for the analysis of native proteoforms and for determining the composition of protein complexes (see Supplemental Discussion 4 (SD.4)). Other topics discussed in more detail in the supplement include: (SD.1) Deconvolution strategies of fragmentation data; (SD.2) the calculation of a precise mass shift from the fragmentation data; (SD.3) interrogation of histone H3 datasets for fragments containing and acetylation site; (SD.5) and introductions to the discovery/validation resource, TDVALIDATOR; (SD.6) an introduction to a proteoform database generation tool, PROTEIN ANNOTATOR; (Table S1) and an overview of existing open-access, freeware and commercial resources commonly used for nTDMS.