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.

Pechan and Gwaltney BMC Bioinformatics 2012 13(Suppl 15):S13   doi:10.1186/1471-2105-13-S15-S13

Open Data