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

BMC Bioinformatics

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.

ISSN: 1471-2105