Xisearch calculates a series of subscores for each CSM and combines (most of) these into the final score. The following table gives an overview of most of these
Explanations for most scores:
| Score | Description | Source | Search-Library Dependent | Peptide1 | Peptide2 | Both Peptides | total | Non-Lossy/primary | Lossy | Conservative | Absolute | Relative | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fragments | |||||||||||||
| matched | number of fragments matched Each fragment is only counted ones - no independent of how often it is seen | FragmentCoverage | x | x | x | x | x | x | x | x | x | ||
| unique matched | same as "matched" but if a peak has more than one fragment matched to it, only one explanation is counted | x | x | x | x | x | x | x | x | x | |||
| multi matched | how many of the possible fragments where observed in more than one charge state | x | x | x | x | x | |||||||
| fragment CCPepStubCount | how many peptides are seen with crosslinker stub (0,1 or 2) | x | |||||||||||
| fragment CCPepDoubletCount | how many peptides are seen with crosslinker stub pairs (0,1 or 2) | x | |||||||||||
| sequencetag coverage | How much of the peptide is explained by consecutive fragments (minumum 3 consecutive fragments make a tag) | SequenceTagCoverage | x | x | x | x | |||||||
| MaxCharge | Maximum charge of any fragment matched | FragmentChargeState | x | x | x | ||||||||
| MedianCharge | Median Charge any fragment matched | x | x | x | |||||||||
| AverageCharge | Average charge any fragment matched | x | x | x | |||||||||
| Spectrum | |||||||||||||
| spectrum peaks explained | how many of the peaks in the spectra are explained by the current match | SpectraCoverage | x | ||||||||||
| specrum intensity explained | how much of the intensity is explained by the current match | SpectraCoverage/SpectraCoverageConservative | x | x | x | ||||||||
| spectrum Top10 matched % | SpectraCoverage | x | |||||||||||
| spectrum Top10 matched % | x | ||||||||||||
| spectra top20 matched% | x | ||||||||||||
| spectra top40 matched% | x | ||||||||||||
| spectra matched single% | how much of the intensity all peaks without isotope cluster are explained | x | |||||||||||
| spectra matched isotop% | how much of the intensity all peaks with isotope cluster are explained | x | |||||||||||
| spectra isotop% | how much of the spectrum intensity is contained in isotop clusters | x | |||||||||||
| Errors | |||||||||||||
| Average MS2 error | Error | x | x | ||||||||||
| Average1-RelativeMS2Error | Avaerage of 1-(MS2Error/MaximalPermitedError) | x | |||||||||||
| Precoursor Error | x | x | |||||||||||
| 1-ErrorRelative | 1-Precursor Error | x | |||||||||||
| SearchLibraryScore | |||||||||||||
| mgcAlpha | Candidate Score for the alpha peptide -loge(Π(peptides matching peak/number off all fragments)) | no group | x | x | |||||||||
| mgcBeta | Candidate Score for the alpha peptide (not used for candidate selecteion) | x | x | ||||||||||
| mgxScore | candidate score for the peptide pair | x | x | ||||||||||
| mgxRank | the ranking in the list of mgx-candidates | x | x | ||||||||||
| mgcScore | mgcAlpha+mgcBeta | x | x | ||||||||||
| mgcDelta | difference to the second best mgc score | x | |||||||||||
| FragmentLibraryScore | similare to mgxscore but on whole spectrum instead of a denoised version | FragmentLibraryScore | x | ||||||||||
| FragmentLibraryScoreExponential | scaleing of FragmentLibraryScore | FragmentLibraryScore | x | ||||||||||
| FragmentLibraryScoreLog | scaleing of FragmentLibraryScore | FragmentLibraryScore | x | ||||||||||
| Other | |||||||||||||
| SpectrumQualityScore | combines several spectrum related scores to provide some inkling of how good the spectrum is matched and how good the spectrum itself is | CombineScore | |||||||||||
| betaCount | for the given alpha peptide how many beta peptides would match the gap-mass | NoGroup | |||||||||||
| betaCountInverse | 1/betaCount | ||||||||||||
| Autovalidation | Passes autovalidation | ||||||||||||
| LinkSiteDelta | how much better is the linksite then any other site (0 means its ambigious) | ||||||||||||
| match score | final score | x | |||||||||||
| delta | diferrence to the secon best final score | ||||||||||||
| MatchScore | to be ignored | ||||||||||||
| J48ModeledManual001 | to be ignored | ||||||||||||
| AllScore | to be ignored | ||||||||||||
| MeanSquareRootError | to be ignored | ||||||||||||
| MeanSquareError | to be ignored | ||||||||||||
| Modified | to be ignored | ||||||||||||
| Containing | to be ignored | ||||||||||||
| Crosslinked | to be ignored | ||||||||||||
| BS3ReporterIonScore | to be ignored |
columns:
- Source : where it is calculated (not really of interest here)
- Search-Library Dependent : these scores depend on the fasta and modification settings. i.e. if you search the same data with a different e.g. a larger or smaller database even a match between the same peptides and the same spectrum will have somewhat different values.
- Peptide1 : score exists as a version for peptide 1
- Peptide2 : score exists as a version for peptide 2
- Both Peptides: score exists as a version combining peptide 1 and 2
- total: every ion is counted - independent whether it is a neutral loss or not. E.g. a peak matched with y5+loss of water would count as y5 seen.
- Non-Lossy/primary: only basic ions (a,b,c,x,y,z) are counted - e.g. a peak matched to y5 counts as y5 seen, but y5+loss of water would not count
- Lossy: coutns only how many fragments are seen as neutral loss. e.g. y5 does not count but y5+loss of water does
- Conservative: every basic ion counts but also if a basic ion is not seen however three or more distinct versions with losses are seen count. E.g. if y5 is matched it counts but also y6 with 1 loss of water + y6 with 2 loss water and y6 with 3 loss of water seen would count as y6 seen.
- Absolute: absolute values taken (think of errors +5 ppm error and +5 ppm error are considered the same.
- relative: also taken as fraction of theoretical maximum. e.g. an error of 2ppm when searched with a maximum erro of 10 ppm would be 0.2 or seen 4 fragments matched for a 9 aminoacid long peptide would be 4/((9-1)*2)=0.25