Predict MS/MS spectra using the kinetic model - BioPharma Finder Software - Peptide Mapping Analysis User Guide - Predict MS/MS spectra using the kinetic model - View Peptide Mapping Analysis results - Process and Review page - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. For a Peptide Mapping Analysis experiment, you have processed your experiment and are viewing the results on the Process and Review page.

Procedure

1. On the Process and Review page, select the MS2 Spectra subtab.
2. Select a row in the Results table that displays "MS2" in the ID Type column.
3. Right-click the MS2 Spectra pane and select Predict Peptide MS/MS (Kinetic Model).
4. The application opens the Predict Peptide MS/MS (Kinetic Model) dialog box.
4. In the Sequence box, type the one-letter codes for a peptide sequence.
5. See Amino acid letter codes.
6. Use uppercase when typing the one-letter codes.
7. In addition to the standard one-letter peptide codes, the following special peptide codes are accepted:
8. •D for deamidated asparagine
9. •J for carboxymethylated cysteine
10. •U for carboxyamidomethylated cysteine
11. •O for oxidized methionine
12. •S for phosphorylated serine
13. Additionally, you can indicate modifications by typing the modification in parentheses after the sequence.
14. For example, AADECFGHK(C5+250)(H8−9) means the cysteine at position 5 is modified by +250 u and the histidine at position 8 is modified by −9 u.
15. Another example: AANASAA(N3+A2G0F) means the asparagine at position 3 is glycosylated with glycan A2G0F.
16. To define a disulfide bond, type the bond in parentheses.
17. For example: ADCAGHTYCHPEK(C3−C9) means the cysteine at position 3 and the cysteine at position 9 are linked by a disulfide bond.
5. Enter values for the following parameters:
1. To set the charge state, the isolation width used for fragmentation, the resolution at m/z = 400, and the activation time (ms), enter a value in their boxes.
2. To define a fragmentation method, select from the available options in the list.
3. To select an instrument, select an instrument name from the list.
4. To define the collision energy or reagent target, enter a value in the box.
5. Specify normalized collision energy as a percentage value (%) or specify the reagent ion target value for the ETD fragmentation method.
6. Select OK to view the predicted MS/MS spectrum.
7. The application displays the changes in the predicted spectrum in the MS2 Spectra pane.
8. See View the predicted and experimental MS/MS spectra.

9. NOTE

   For components identified as dimers, the resulting predicted MS/MS spectrum using the kinetic model will not be correct.