## 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 | kojak | percolator | spectral-counts | ||
---|---|---|---|---|---|---|---|---|---|

PSM | peptides | proteins | |||||||

file | The name of the file containing the scan. | ✓ | ✓ | ||||||

fileidx | 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 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
maximum 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` . |
✓ | ✓ | ||||||

res-ev p-value | The high-resolution p-value computed as described in
"Combining High-Resolution and Exact Calibration to Boost Statistical Power:
A Well-Calibrated Score Function for High-Resolution MS2 Data".
This column only appears when `--score-function=both` or
`--score-function=residue-evidence` . In addition,
`exact-p-value=T` . |
✓ | ✓ | ||||||

res-ev p-score | The high-resolution score computed as described in
"Combining High-Resolution and Exact Calibration to Boost Statistical Power:
A Well-Calibrated Score Function for High-Resolution MS2 Data".
This column only appears when `--score-function=both` or
`--score-function=residue-evidence` . |
✓ | ✓ | ||||||

combined p-value | The high-resolution p-value computed as described in
"Combining High-Resolution and Exact Calibration to Boost Statistical Power:
A Well-Calibrated Score Function for High-Resolution MS2 Data".
This column only appears when `--score-function=both` and
`--exact-p-value=T` . |
✓ | ✓ | ||||||

xcorr rank | The rank of this PSM when sorted by xcorr. | ✓ | ✓ | ✓ | |||||

res-ev rank | The rank of this PSM when sorted by res-ev score or by res-ev p-value. | ✓ | ✓ | ||||||

combined p-value rank | The rank of this PSM when sorted by combined p-value. | ✓ | ✓ | ||||||

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. | ✓ | ✓ | ✓ | |||||

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. | ✓ | |||||||

peptides-scan.charge | Peptides belonging to each protein in the group, with scan and charge (for example, EAMPK-001285.2) | ✓ | |||||||

Scan Number | The identifying number of each scan. | ✓ | |||||||

Ret Time | The retention time in minutes. | ✓ | |||||||

Obs Mass | The observed mass of the precursor ion peak. | ✓ | |||||||

PSM Mass | The theoretically computed precursor mass of the PSM. | ✓ | |||||||

PPM Error | The difference (in parts per million) between the PSM mass and the Obs Mass. | ✓ | |||||||

Score | The Kojak cross-correlation score. | ✓ | |||||||

dScore | The difference between the reported PSM score and the next best PSM score. | ✓ | |||||||

E-value | The overall E-value of the PSM. | ✓ | |||||||

Peptide #1 Score | The Kojak xcorr score of the higher scoring peptide. | ✓ | |||||||

Peptide #1 E-value | The E-value of the higher scoring peptide. | ✓ | |||||||

Peptide #1 | The peptide sequence of the higher scoring peptide. | ✓ | |||||||

Linked AA #1 | The site of the cross-link in Peptide #1 | ✓ | |||||||

Protein #1 | The protein(s) that generated Peptide #1. | ✓ | |||||||

Protein #1 Site | The site(s) of the cross-link in Protein #1 | ✓ | |||||||

Peptide #2 Score | The Kojak xcorr score of the lower scoring peptide. | ✓ | |||||||

Peptide #2 E-value | The E-value of the lower scoring peptide. | ✓ | |||||||

Peptide #2 | The peptide sequence of the lower scoring peptide. | ✓ | |||||||

Linked AA #2 | The site of the cross-link in Peptide #2 | ✓ | |||||||

Protein #2 | The protein(s) that generated Peptide #2. | ✓ | |||||||

Protein #2 Site | The site(s) of the cross-link in Protein #2 | ✓ | |||||||

Linker Mass | The mass contribution of the cross-linker for cross-linked PSMs or zero otherwise. | ✓ |