In bottom‑up proteomics, peptides are analyzed in a mass spectrometer, usually to infer information about the proteins they come from. When you analyse your mass spectrometer results in Spectronaut or SpectroDive, 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 post-translationally modified status of the peptides. In our reports, this appears as the additional mass added ‑if any‑ to the amino acid residue in square brackets.
  • Precursor: this 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.

Following this rationale, the number of precursors will always be equal or higher than the number of modified peptides, and the latter equal or higher than the number of stripped sequences (or peptides, table 1).


Spectronaut allows choosing which if these elements are considered as "peptides" for reporting purposes and used to quantify proteins. Read about it here.



Related content:

How does Spectronaut™ calculate the quantitative values?

What does the qvalue for peptide and protein mean?




Created by SEZ. Last update 2018-03-14 by SEZ