Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences

Table 1 Modifications and spectral pairs found in data set 1

Δm(Da)		ΔRt(Scans)		# of spectral pairs (pp> 0.98)*	Modification type	Theoretical mass (Da)	Unimod AC #
Mean	± 3Sigma	Mean	± 3Sigma
57.0221	± 0.0186	-31.4	± 387.1	2303	Carbamidomethylation	57.0215	4
21.9839	± 0.0108	-10.5	± 276.2	319	Cation:Na	21.9819	30
17.0254	± 0.0201	-353. 2	± 1360.0	0	Ammonia-loss/Gln → pyro-Glu	17.0265	385/28
14.0157	± 0.0178	-677.6	± 1012.6	0	Methylation/Asp → Glu	14.0157	34/558
0.98943	± 0.0603	176.6	± 1152.6	0	Amidation/Deamidation	0.98402	2/7

*pp stands for the posterior probability of being modification-related. 3Sigma stands for three times of standard deviation. For the last three modifications, spectral pairs of pp > 0.98 are not detected out. This is due to the less abundance of these modifications. However, this does not prevent the algorithm from accurately estimating their masses.

ISSN: 1471-2105