Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide

BMC Bioinformatics

Table 1 Experimental and predicted ion intensities in the MSMS spectra of the doubly charged GAVLK peptide.

Protonated isomers	ions	Experimental intensity order	Predicted order*	Averaged experimental relative intensity CID and PQD	Predicted relative intensity DFT EHC	Predicted relative intensity DFT E	Predicted relative intensity DFT GE	Predicted relative intensity DFT GEEC
GAVLK_NH_2	y4	4	4	0.0095	0.0102	0.0203	0.0186	1.0500(1)
GAVLK_NH_3	y3	1	1	1.0000	1.0000	1.0000	1.0000	1.0000(2)
GAVLK_NH_4	y2	2	2	0.1405	0.1780	0.2902	0.0945	0.0083(3)
GAVLK_NH_5	y1	3	3	0.0451	0.0382	0.0438	0.0003	0.00004(4)
GAVLK_NH_2	b1	ND	4
GAVLK_NH_3	b2	1	1	Sum of logErr:	0.2076	0.6549	2.6428	6.3255
GAVLK_NH_4	b3	2	2
GAVLK_NH_5	b4	3	3

Boltzmann distributions were based on the free energies of all the low energy (within 20 kJ.mol^-1 of the lowest) conformers calculated as follows: EHC - DFT energy with enthalpic corrections; E - DFT energy; GE- Gibbs free energy; except for GEEC, when the Gibbs free energy of a single equilibrium conformer for each isomer was used. The calculations for GAVLK_NH_1 isomers energies were not considered, because that particular protonation does not lead to fragmentation and as such is inconsequential. ND - not detected; logErr - decadic logarithm of relative error.
* The predicted order for the GEEC calculations is given in parenthesis in the pertinent column.

ISSN: 1471-2105