Computational Proteomics: Mass Spectrometry Peptide-to-spectrum assignment and MS1 feature finding and alignment
Mass spectra have to be matched with the corresponding originating peptides making use of the algorithms called search engines in a process that can be very computationally demanding. The masses of the peptides fragments are compared to theoretically derived fragments masses from peptides sequences stored in a database and are assigned a score or probability that the peptide sequence actually generates the spectrum. In addition quantitative data can be generated from the MS data since the intensity of the intact peptides can be used to infer the original protein abundance. To do so, peptide 'features' can be extracted from the MS1 map that represents an MS run relating chromatographic retention time and mass-to-charge values. These peptide-like signals might be present with different intensities across different MS runs, so by aligning them and extrapolating the peptide sequences that the search engines annotate them, it is possible to estimate eventually protein abundances across different experiments.