Interpreting Scores From Ms/Ms Search - Agilent Technologies Spectrum Mill MS G2721AA Quick Start Manual

Interpreting scores from MS/MS Search

The following definitions and guidelines will help you evaluate your MS/MS search
results:
Peptide score
Score of an individual peptide. This score reflects the information content
(amount of useful fragmentation) in the MS/MS spectrum.
Protein score
Score of the overall protein, calculated by adding scores of all the peptides
detected for the protein
• Scores greater than 25 almost always represent valid results.
% SPI
Percentage of the extracted MS/MS ion current explained by theoretical
fragmentation of the database hit
Guidelines for validating ion trap results based on MS/MS Search scores
Peptide
score
13-25
9-13
6-9
3-6
Guidelines for validating Agilent Q-TOF results based on MS/MS Search scores
Because the mass accuracy is better than with ion trap data, you search with a
narrower mass tolerance, so there is a better chance that lower-scoring results are
valid.
When you manually validate, apply the following filters in Protein/Peptide
Summary:
• Peptide score > 5
• % SPI > 60
16
Quality Peptide
fragmentation
Excellent Extensive
Good Substantial
Mediocre Moderate
Weak Sparse
Likelihood of valid interpretation
When combined with % SPI of 70 or
greater, very likely to be valid
When combined with % SPI of 70 or
greater, likely to be valid
Review results to determine whether
interpretation is valid
Not likely to be valid
Spectrum Mill Workbench Quick Start Guide