Peptide, modified peptide and precursor

Peptide, modified peptide and precursor

In bottom‑up proteomics peptides are analyzed in a mass spectrometer, usually 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).

  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.
  2. Modified peptide: it reports information about the posttranslational 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.
  3. 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 rational, 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).



    • Related Articles

    • 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 ...
    • Qvalue sparse, complete, and percentile: what's the difference?

      Qvalues can be used to filter your data according to the error rate among your accepted entries. For example, if you set a threshold of Qvalue ≤ 0.01, you are applying an FDR threshold of 1%. Biognosys' software uses Qvalues for two different ...
    • How is my data normalized in Spectronaut™?

      Why normalization? The aim of data normalization in proteomics is to correct for the variability that is not coming from the biological system itself but from the experimental process, mainly multistep sample preparation, and LC-MS instrumentation, ...
    • What are MRM and PRM?

      Multiple reaction monitoring (MRM), also known as selected reaction monitoring (SRM), and parallel reaction monitoring (PRM) are targeted proteomics technologies aimed at quantifying up to hundreds of proteins in the same experiment. Multiple ...
    • What are MRM and PRM?

      Multiple reaction monitoring (MRM), also known as selected reaction monitoring (SRM), and parallel reaction monitoring (PRM) are targeted proteomics technologies aimed at quantifying up to hundreds of proteins in the same experiment. Multiple ...