Features used by percolator and q-ranker
Following is a list of the features used by the crux percolator and crux q-ranker commands to represent each peptide-spectrum match (PSM).
| Number | Name | Type | Description | Percolator | q-ranker | barista |
|---|---|---|---|---|---|---|
| 1 | lnrSp |
Float | The natural logarithm of the rank of the match based on the Sp score | ✓ | ||
| 2 | deltLCn |
Float | The difference between this PSM's XCorr and the XCorr of the last-ranked PSM for this spectrum, divided by this PSM's XCorr or 1, whichever is larger. | ✓ | ||
| 3 | deltCn |
Float | The difference between this PSM's XCorr and the XCorr of the next-ranked PSM for this spectrum, divided by this PSM's XCorr or 1, whichever is larger. Note that this definition differs from that of the standard delta Cn reported by SEQUEST®. | ✓ | ✓ | ✓ |
| 4 | Xcorr / XCorr Score |
Float | The SEQUEST cross-correlation score | ✓ | ✓ | ✓ |
| 5 | Sp / Sp score |
Float | The preliminary SEQUEST score. | ✓ | ✓ | ✓ |
| 6 | IonFrac |
Float | The fraction of b and y ions theoretical ions matched to the spectrum | ✓ | ||
| 7 | Mass |
Float | The observed mass [M+H]+ | ✓ | ✓ | ✓ |
| 8 | PepLen |
Integer | The length of the matched peptide, in residues | ✓ | ✓ | ✓ |
| 9-11 | Charge[n] |
Boolean | Is this a 1+/2+/3+ charged spectrum? | ✓ | ✓ | ✓ |
| 12 | enzN |
Boolean | Is the peptide preceded by an enzymatic (tryptic) site? | ✓ | ✓ | ✓ |
| 13 | enzC |
Boolean | Does the peptide have an enzymatic (tryptic) C-terminus? | ✓ | ✓ | ✓ |
| 14 | enzInt |
Integer | Number of missed internal enzymatic (tryptic) sites | ✓ | ||
| 15 | lnNumSP |
Float | The natural logarithm of the number of database peptides within the specified precursor range | ✓ | ||
| 16 | dM |
Float | The difference between the calculated and observed mass | ✓ | ||
| 17 | absdM |
Float | The absolute value of the difference between the calculated and observed mass | ✓ | ||
| 18 | label |
Boolean | Is this decoy or target? | ✓ | ✓ | |
| 19 | xcorr rank |
Integer | The rank of this PSM when sorted by xcorr | ✓ | ✓ | |
| 20 | Sp rank |
Integer | The rank of this PSM when sorted by sp score. | ✓ | ✓ | |
| 21 | missed cleavage |
Boolean | Does the peptide contain one or more missed cleavage sites? | ✓ | ✓ | |
| 22 | number of sequence comparisons |
Integer | The number of sequence comparisons | ✓ | ✓ | |
| 23 | delta mass |
Float | Difference between measured and calculated mass | ✓ | ✓ | |
| 24 | abs(delta mass) |
Float | Absolute value of delta mass | ✓ | ✓ | |
| 25 | b ions |
Float | The XCorr from the theoretical b-ions. | ✓ | ✓ | |
| 26 | y ions |
Float | The XCorr from the theoretical y-ions. | ✓ | ✓ | |
| 27 | flanking |
Float | The XCorr from the flanking peaks | ✓ | ✓ | |
| Total | 17 | 20 | 20 |