Txt file format (search-for-xlinks)
The txt file format records the matches between MS/MS spectra and a sequence database using lines of tab delimited fields.
A txt file consists of a single line containing the names of fields separated by tabs, followed by one or more lines giving the field values separated by tabs.
List of fields
Additional fields for qvalues.target.txt
- 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.
- peptide mass mono: The computed mono-isotopic mass of the peptide sequence (sum of the amino acid masses).
- peptide mass average: The computed average mass of the peptide sequence (sum of the amino acid masses).
- mass error(ppm): The mass error between the mono-isotopic peptide mass and the spectrum neutral mass (ppm).
- xcorr score: The SEQUEST-type cross correlation score.
- 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.
- matches/spectrum: The number of candidate peptides in the database found for this spectrum.
- sequence: The product sequence(s) and link locations.
- protein id: A comma-separated list of proteins in which this peptide appears.
- by total: total number of b-y ions in sequence
- by observable (0-1200): total number of b-y ions observable in the 0-1200 m/z range.
- by observable bin (0-1200): total number of b-y ions observable in the 0-1200 1Da bins.
- by observable (0-max): total number of b-y ions observable in the entire m/z range.
- by obserbable bin (0-max): total number of b-y ions observable in the entire m/z range using 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.
- p-value bonf.: bonferroni corrected p-value
- fdr b-h: false discovery rate calculated by Benjamini & Hochberg algorithm.
- fdr decoy: false discovery rate calculated by target/decoy using p-values.
- q-value b-h: q-value calculated using fdr b-h column.
- q-value decoy: q-value calculated using fdr decoy column.