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Table 2 Improved Peptide Sequence Assignment via De-isotoped MS/MS Spectra.

From: multiplierz: an extensible API based desktop environment for proteomics data analysis

Experiment # Peptides Before Deisotoping # Peptides After Deisotoping # New Peptides % New Peptides
1 218 271 53 31%
2 178 208 30 17%
3 204 250 46 33%
4 379 442 63 34%
5 320 391 71 35%
Average 259.8 312.4 52.6 30%
  1. High resolution Orbitrap HCD MS/MS spectra of high charge state (z > 2+) precursors were frequently not assigned to a peptide sequence due to the presence of multiple isotope peaks per fragment ion. We processed the peak lists (MGF format) using an .mz script to only retain mono-isotopic and singly charged fragment ion peaks. Subsequent research of these data provided an average increase of 30% in the number of high-confidence (Mascot score > 30) peptide assignments across 5 LC-MS runs.