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

  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.
  5. peptide mass mono: The computed mono-isotopic mass of the peptide sequence (sum of the amino acid masses).
  6. peptide mass average: The computed average mass of the peptide sequence (sum of the amino acid masses).
  7. mass error(ppm): The mass error between the mono-isotopic peptide mass and the spectrum neutral mass (ppm).
  8. xcorr score: The SEQUEST-type cross correlation score.
  9. xcorr rank: The rank of this PSM when sorted by xcorr.
  10. p-value: The p-value computed from the estimated Weibull parameters of the score distribution for this spectrum.
  11. matches/spectrum: The number of candidate peptides in the database found for this spectrum.
  12. sequence: The product sequence(s) and link locations.
  13. protein id: A comma-separated list of proteins in which this peptide appears.
  14. by total: total number of b-y ions in sequence
  15. by observable (0-1200): total number of b-y ions observable in the 0-1200 m/z range.
  16. by observable bin (0-1200): total number of b-y ions observable in the 0-1200 1Da bins.
  17. by observable (0-max): total number of b-y ions observable in the entire m/z range.
  18. by obserbable bin (0-max): total number of b-y ions observable in the entire m/z range using bins.
  19. by observed bin: total number of b-y ions observed in spectrum
  20. ion current total: total ion current for spectrum
  21. ion current observed: total ion current observed for matching b-y ions
  22. ions observable bin (0-1200): total ions observable (b-y, flanks, and neutral losses) within 0-1200 m/z range.
Additional fields for qvalues.target.txt
  1. p-value bonf.: bonferroni corrected p-value
  2. fdr b-h: false discovery rate calculated by Benjamini & Hochberg algorithm.
  3. fdr decoy: false discovery rate calculated by target/decoy using p-values.
  4. q-value b-h: q-value calculated using fdr b-h column.
  5. q-value decoy: q-value calculated using fdr decoy column.

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