Tab-delimited file format
Various programs in Crux report their output and read inputs in tab-delimited text format. Each such file consists of a single line containing the tab-separated names of fields, followed by one or more lines giving the corresponding field values.
Name Description comet tide search-for-xlinks search-for-xlinks (new) barista q-ranker percolator spectral-counts PSM peptides proteins sub-proteins PSM peptides proteins 1 scan The identifying number of each scan ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 2 charge The charge state for this spectrum in this PSM. ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 3 spectrum precursor m/z The observed m/z of the spectrum precursor ion. ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 4 spectrum neutral mass The computed mass of the spectrum precursor at the given charge state. This is equal to the precursor m/z minus the mass of a proton (1.00727646677 Da), all multiplied by the charge. ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 5 peptide mass The mass of the peptide sequence, computed as the sum of the the amino acid masses plus the mass of water (18.010564684 Da or 18.0153 Da, depending on whether we are using monoisotopic or average mass). ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 6 delta_cn The normalized difference in xcorr for this PSM relative to other PSMs for this spectrum at this charge state. ✓ ✓ ✓ ✓ ✓ ✓ 7 sp score The SEQUEST-type preliminary score. ✓ ✓ ✓ ✓ ✓ 8 sp rank The rank of this PSM when sorted by Sp score. Note that, in tide-search, the Sp score is only computed for PSMs that are reported to the user. Hence, the rank of the Sp score will be in the range from 1 to n, where the value of n is determined by the--top-matchparameter.✓ ✓ ✓ ✓ ✓ 9 xcorr score The SEQUEST-type cross correlation score. This column only appears when exact-p-value=F.✓ ✓ ✓ ✓ ✓ ✓ ✓ 10 exact p-value The p-value computed as described in "Computing Exact p-values for a Cross-correlation Shotgun Proteomics Score Function". This column only appears when exact-p-value=T.✓ 11 refactored xcorr A discretized version of XCorr, used to compute the p-value. This column only appears when exact-p-value=T.✓ 12 xcorr rank The rank of this PSM when sorted by xcorr. ✓ ✓ ✓ ✓ ✓ ✓ ✓ 13 p-value The p-value computed from the estimated Weibull parameters of the score distribution for this spectrum. ✓ ✓ ✓ 14 percolator score The discriminant score assigned by percolator. ✓ ✓ ✓ 15 percolator rank The rank of this PSM, peptide or protein when sorted by percolator score. ✓ ✓ ✓ 16 percolator q-value The q-value assigned by percolator. ✓ ✓ ✓ 17 q-ranker score The discriminant score assigned by q-ranker. ✓ 18 q-ranker q-value The q-value assigned by q-ranker. ✓ 19 q-ranker PEP The posterior error probability estimated from the q-ranker score ✓ 20 barista score The discriminant score assigned by barista. ✓ ✓ ✓ 21 barista q-value The q-value assigned by barista. ✓ ✓ ✓ 22 barista PEP The PEP assigned by barista ✓ ✓ 23 b/y ions matched The number of b-ions and y-ions in the peptide that have a corresponding peak in the spectrum. ✓ ✓ ✓ ✓ 24 b/y ions total The total number of b- and y-ions predicted for this peptide. ✓ ✓ ✓ ✓ ✓ ✓ 25 total matches/spectrum The number of candidate peptides in the database found for this spectrum, including duplicates. Note that this is always the number of target candidate peptides, even if the PSM involves a decoy peptide. ✓ ✓ ✓ 26 distinct matches/spectrum The number of unique candidate peptides in the database found for this spectrum. Note that this is always the number of target candidate peptides, even if the PSM involves a decoy peptide. ✓ ✓ ✓ ✓ ✓ ✓ ✓ 27 sequence The peptide sequence. ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 28 cleavage type The cleavage rules for generating this peptide based on the user-specified enzyme specificity. ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 29 protein id A comma-separated list of proteins in which this peptide appears. Optionally, the protein name may be followed by a number in parentheses giving the start position of the peptide in the protein. ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 30 flanking aa The amino acids that precede and follow this peptide in the parent protein ID. ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 31 RAW The raw (unnormalized) count of spectra per peptide ✓ 32 SIN A protein quantification score ✓ 33 NSAF The normalized spectral abundace factor ✓ ✓ ✓ 34 dNSAF The distributed normalized spectral abundace factor ✓ 35 EMPAI The exponentially modified protein abundance index ✓ 36 parsimony rank The protein rank based on its spectral-counts score. ✓ 37 filename The name of the file in which the PSM appears. ✓ ✓ ✓ 38 psm_id PSM identifier. ✓ 39 protein group number Protein group index ✓ 40 peptides-scan.charge Peptides belonging to each protein in the group, with scan and charge (for example, EAMPK-001285.2) ✓ ✓ ✓ 41 proteins Proteins in the protein group. Each protein can be followed by peptides in parenthesis, if they belong only to this particular protein in the group. Since peptides are considered indistinguishable if they have identical amino acid sequences or they differ only by I/L or T/S in the same position in the peptide, the peptides shared by the group may not all be identical. ✓ ✓ 42 parent group numbers The numbers of the protein groups in the barista.target.proteins.txt that are supersets of this group in terms of peptides. ✓ 43 peptide mass mono Monoisotopic peptide mass ✓ 44 peptide mass average Average peptide mass ✓ 45 mass error(ppm) The mass error (in ppm) between the observed precursor mass and the cross-link peptide product ✓ 46 protein id(loc) List of protein IDs that give rise to the first and second peptide in the cross-link peptide product. (loc) indicates the location of the peptide in the protein. The ";" separates the protein ids from the first and second peptide. ✓ 47 protein id(loc) 1 List of protein IDs that give rise to the first peptide in the cross-link peptide product. (loc) indicates the location of the peptide in the protein ✓ 48 protein id(loc) 2 List of protein IDs that give rise to the second peptide in the cross-link peptide product. (loc) indicates the location of the peptide in the protein ✓ 49 by total Total number of b-y ions in product ✓ 50 by observable (0-1200) Total number of b and y ions observable in the 0-1200 m/z range ✓ 51 by observable bin (0-1200) Total number of b and y ions observable in the 0-1200 m/z range using 1 Da bins ✓ 52 by observable (0-max) Total number of b and y ions observable in the entire m/z range ✓ 53 by observable bin (0-max) Total number of b and y ions observable in the entire m/z range using 1 Da bins ✓ 54 by observed bin Total number of b-y ions observed in spectrum ✓ 55 ion current total Total ion current for spectrum ✓ 56 ion current observed Total ion current observed for matching b-y ions ✓ 57 ions observable bin (0-1200) Total ions observable (b, y, flanks, and neutral losses) within 0-1200 m/z range ✓