Calculating the MS2 Score in the BioPharmaView™ Software for Confident Selection of Peptides for Quantification

For research use only. Not for use in diagnostic procedures.

Answer

In BioPharmaView™ software, the MS2 score evaluates the quality of a match between MS/MS peaks and a set of theoretical fragments. The MS2 score is based on the probability of the MS/MS peaks matching the set of theoretical fragments of the molecule by chance. The score is calculated automatically by the software as follows:

Score = -log10(p – value)

The auto-validation threshold should be set and examined using the Optimize Matching Parameters window in the BioPharmaView software, and an acceptable false discovery rate (FDR) is selected. The FDR for BioPharmaview is described in this link: https://sciex.com/support/knowledge-base-articles/how-is-the-fdr-calculated-in-the-peptide-spectrum-matching-step-in-the-biopharmaview-software_en_us

This leads to the question, “How are peptides selected for quantification?” If users choose peptides manually from an information-dependent acquisition (IDA) or data-dependent acquisition (DDA) experiment, what guidelines should be followed to select the best peptides for quantification?

One consideration when selecting a peptide is determining the abundance of that peptide in its modified and unmodified forms. In BioPharmaView software, the percent modification for a given peptide is shown in a results table. Additional criteria - such as the presence of multiple charge states, the quality of the MS/MS spectra and the retention time - also appear in the results table to help users decide which peptides are best for quantification. Other features in the results table, can also be used when selecting a peptide:

• Green check marks indicate if a peptide is validated when used to calculate a percent modification. 
• A "MS/MS evidence" column represents the MS/MS spectral quality; scores above the set threshold will be auto-validated.
• The “Use” checkmark can be deselected for a particular match if it should not be used in a calculation.