Features used by percolator and q-ranker
Following is a list of the features used by the
crux percolator
andcrux 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
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