## Features used by Percolator, Q-ranker, and Barista

Following is a list of the features used by the crux percolator, crux q-ranker, and crux barista 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 |
15 |
18 |
18 |