proteomics studies the identities, amounts, modifications and associations of proteins in biological material. Measurements depend on extraction, detectability and reference condition; absence of a detected peptide is not proof that its protein is absent.
Proteome-scale assignment of proteins to cellular locations using fractionation profiles, localization labeling and complementary imaging.
Analysis of relatively large protein fragments to preserve linkage between sequence changes or modifications that separate into different peptides in bottom-up proteomics. It generally preserves less complete linkage than intact-chain analysis.
Analysis of intact protein ions and their sequence fragments to characterize proteoforms. Intact mass constrains composition, while informative fragmentation is needed to locate changes and resolve many isomeric forms.
An error in assigning a complete molecular form. Controlling peptide-level identification error does not automatically control errors in intact-form identity or modification linkage.
Analysis of proteins after digestion into smaller peptides. It can provide broad sequence and modification coverage, but digestion commonly loses information about which distant variations occur together in an intact proteoform.
A molecular form of a protein defined by its amino-acid sequence and covalent modifications, including processing. Different conformations and mass-spectrometric charge states do not by themselves define different proteoforms.
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The study of the proteome.