Table 2

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

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%

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.

Parikh et al. BMC Bioinformatics 2009 10:364   doi:10.1186/1471-2105-10-364