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