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	cascade-search	search-for-xlinks	search-for-xlinks (new)	barista				q-ranker	percolator			spectral-counts
							PSM	peptides	proteins	sub-proteins		PSM	peptides	proteins
file	The name of the file containing the scan.		✓	✓	✓	✓
file	The integer index of the file containing the scan.											✓
scan	The identifying number of each scan.	✓	✓	✓	✓	✓	✓	✓			✓	✓	✓
charge	The charge state for this spectrum in this PSM.	✓	✓	✓	✓	✓	✓	✓			✓	✓	✓
spectrum precursor m/z	The observed m/z of the spectrum precursor ion.	✓	✓	✓	✓	✓	✓	✓			✓	✓	✓
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.	✓	✓	✓	✓	✓	✓	✓			✓	✓	✓
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).	✓	✓	✓		✓	✓	✓			✓	✓	✓
delta_cn	The normalized difference in XCorr for this PSM relative to the next ranked PSM for the same spectrum and charge. The denominator for normalization is the minimum of the current XCorr and 1.0. If exact-p-value=T, then the difference is computed between -log(p-value) rather than XCorr, and no normalization is applied.	✓	✓	✓		✓	✓	✓			✓
delta_lcn	Similar to delta_cn, except that the difference is computed with respect to the lowest reported XCorr score for a given spectrum and charge state.		✓
sp score	The SEQUEST-type preliminary score.	✓	✓	✓			✓	✓			✓
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-match parameter.	✓	✓	✓			✓	✓			✓
xcorr score	The SEQUEST-type cross correlation score. This column only appears when exact-p-value=F.	✓	✓	✓	✓	✓	✓	✓			✓
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.		✓	✓
refactored xcorr	A discretized version of XCorr, used to compute the p-value. This column only appears when exact-p-value=T.		✓	✓
xcorr rank	The rank of this PSM when sorted by xcorr.	✓	✓	✓	✓	✓	✓	✓			✓
p-value	The p-value computed from the estimated Weibull parameters of the score distribution for this spectrum.				✓	✓					✓
percolator score	The discriminant score assigned by percolator.											✓	✓	✓
percolator q-value	The q-value assigned by percolator.											✓	✓	✓
percolator PEP	The posterior error probability assigned by percolator.											✓	✓	✓
q-ranker score	The discriminant score assigned by q-ranker.										✓
q-ranker q-value	The q-value assigned by q-ranker.										✓
q-ranker PEP	The posterior error probability estimated from the q-ranker score										✓
barista score	The discriminant score assigned by barista.						✓	✓	✓
barista q-value	The q-value assigned by barista.						✓	✓	✓
barista PEP	The PEP assigned by barista						✓	✓
b/y ions matched	The number of b-ions and y-ions in the peptide that have a corresponding peak in the spectrum.		✓		✓		✓			✓
b/y ions total	The total number of b- and y-ions predicted for this peptide.	✓	✓		✓		✓	✓			✓
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.	✓			✓							✓
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.		✓	✓	✓	✓	✓	✓			✓	✓
sequence	The peptide sequence, not including any modifications.	✓	✓	✓	✓	✓	✓				✓	✓	✓
modified sequence	The peptide sequence, with modifications included.	✓
modifications	Variable modifications applied to the sequence.		✓	✓
cleavage type	The cleavage rules for generating this peptide based on the user-specified enzyme specificity.	✓	✓	✓	✓	✓	✓	✓			✓	✓	✓
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.	✓	✓	✓	✓	✓	✓	✓			✓	✓	✓	✓	✓
flanking aa	The amino acids that precede and follow this peptide in the parent protein ID. If the peptide occurs in more than one protein, then this column will contain a comma-separated list of pairs of amino acids.	✓	✓	✓	✓	✓	✓	✓			✓	✓	✓
original target sequence	The unmodified target sequence. For a target PSM, the value in this column will be identical to the value in the "sequence" column. For a decoy PSM, this column will contain the corresponding target sequence.		✓		✓	✓
RAW	The raw (unnormalized) count of spectra per peptide														✓
SIN	A protein quantification score														✓
NSAF	The normalized spectral abundace factor							✓	✓						✓
dNSAF	The distributed normalized spectral abundace factor														✓
EMPAI	The exponentially modified protein abundance index														✓
parsimony rank	The protein rank based on its spectral-counts score.														✓
psm_id	PSM identifier.										✓
protein group number	Protein group index									✓
peptides-scan.charge	Peptides belonging to each protein in the group, with scan and charge (for example, EAMPK-001285.2)								✓	✓				✓
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.								✓	✓
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.									✓
peptide mass mono	Monoisotopic peptide mass				✓
peptide mass average	Average peptide mass				✓
mass error(ppm)	The mass error (in ppm) between the observed precursor mass and the cross-link peptide product				✓
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.					✓
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				✓
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			✓
by total	Total number of b-y ions in product				✓
by observable (0-1200)	Total number of b and y ions observable in the 0-1200 m/z range				✓
by observable bin (0-1200)	Total number of b and y ions observable in the 0-1200 m/z range using 1 Da bins				✓
by observable (0-max)	Total number of b and y ions observable in the entire m/z range				✓
by observable bin (0-max)	Total number of b and y ions observable in the entire m/z range using 1 Da bins				✓
by observed bin	Total number of b-y ions observed in spectrum				✓
ion current total	Total ion current for spectrum				✓
ion current observed	Total ion current observed for matching b-y ions				✓
ions observable bin (0-1200)	Total ions observable (b, y, flanks, and neutral losses) within 0-1200 m/z range				✓