Definitions: Peptide, modified peptide and precursor
In bottom-up proteomics, usually peptides are analyzed in a mass spectrometer to infer information about the proteins they come from. When you analyze your mass spectrometry results in any of Biognosys software, you get information for different elements at different levels, related to the detected peptides (Table 1).
Peptide (stripped sequence): it refers to the amino acid sequence regardless of charge state or modification of the analyzed peptide. It is mainly used for protein inference.
Modified peptide: it reports information about the posttranslationally modified status of the peptides. In our reports, this appears with the additional mass added (if any) to the amino acid residue in square brackets.
Precursor: refers to the actual unique molecular unit being analyzed on the mass spectrometer. It contains information about the sequence, the modification status, and the charge state. Ultimately, fragment ions are produced from these precursors.
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