Search Results
Search results can be found in the results.sage.tsv file. The table below describes the columns that are present in this file.
| Header | Description |
|---|---|
peptide | Peptide sequence, including modifications in ProForma format (e.g., NC[+57.021]HKGSFK). |
proteins | Semicolon-delimited list of proteins matching the peptide sequence. |
num_proteins | Number of proteins matching the peptide sequence. |
filename | File containing this PSM |
scannr | Spectrum identifier from mzML file. |
rank | Rank of the PSM. If report_psms > 1, then the best match will have rank = 1, the second best match will have rank = 2, etc. |
label | Target/Decoy label (-1: decoy, 1: target). |
expmass | Experimental mass of the peptide. |
calcmass | Calculated mass of the peptide. |
charge | Reported precursor charge. |
pepide_len | Length of the peptide sequence. |
missed_cleavages | Number of missed cleavages. |
isotope_error | C13 isotope error. |
precursor_ppm | Difference between experimental mass and calculated mass, reported in parts-per-million. |
fragment_ppm | Average parts-per-million (delta mass) for matched fragment ions compared to theoretical ions. |
hyperscore | X!Tandem hyperscore for the PSM. |
delta_next | Difference between the hyperscore of this candidate and the next best candidate. |
delta_bext | Difference between the hyperscore of the best candidate (rank=1) and this candidate. |
rt | Retention time in minutes. |
aligned_rt | Globally aligned retention time. |
predicted_rt | Predicted retention time, if enabled. |
delta_rt_model | Difference between predicted and observed retention time. |
ion_mobility | Ion mobility of the precursor, if present in mzML. |
predicted_mobility | Predicted ion mobility of the precursor, if ion mobility measurements are present in the mzML. |
delta_mobility | Difference between predicted and observed ion mobility. |
matched_peaks | Number of matched theoretical fragment ions. |
longest_b | Longest b-ion series. |
longest_y | Longest y-ion series. |
longest_y_pct | Longest y-ion series, divided by peptide length (as a fraction). |
matched_intensity_pct | Fraction of MS2 intensity explained by matched b- and y-ions (as a percentage of total MS2 intensity for this spectrum). |
scored_candidates | Number of scored candidates for this spectrum. |
poisson | Probability of matching exactly N peaks across all scored candidates (Pr(x=k)). |
sage_discriminant_score | Combined score from linear discriminant analysis, used for FDR (False Discovery Rate) calculation. |
posterior_error | Posterior error probability for this PSM / local FDR. |
spectrum_q | Assigned spectrum-level q-value. |
peptide_q | Assigned peptide-level q-value. |
protein_q | Assigned protein-level q-value. |
ms2_intensity | Total intensity of MS2 spectrum. |