PSM reports

Column contents in the psm.tsv output file is described below:

Spectrum MS/MS spectrum identifier

Spectrum File name of originating identification file

Peptide peptide amino acid sequence, no modifications included

Modified Peptide peptide sequence including modifications

Peptide Length number of residues in the peptide sequence

Charge charge state of the identified peptide

Retention retention time (in seconds)

Observed Mass peptide mass (in Da)

Calibrated Observed Mass peptide mass after calibration (in Da)

Observed M/Z mass-to-charge ratio of the peptide ion

Calibrated Observed M/Z mass-to-charge ratio of the peptide ion after calibration

Calculated Peptide Mass theoretical peptide mass based on identified sequence and modifications

Calculated M/Z theoretical peptide mass-to-charge ratio based on identified sequence and modifications

Delta Mass difference between calibrated observed peptide mass and calculated peptide mass

Expectation expectation value from statistical modeling with PeptideProphet

Hyperscore similarity score between observed and theoretical spectra

Nextscore similarity score of second-highest scoring match for the spectrum

PeptideProphet Probability confidence score determined by PeptideProphet

Number of Enzymatic Termini 2 = fully-enzymatic, 1 = semi-enzymatic, 0 = non-enzymatic

Number of Missed Cleavages number of potential enzymatic cleavage sites within the identified sequence

Intensity relative abundance of the precursor ion

Ion Mobility TIMS transit time of the precursor ion (1/K₀)

Assigned Modifications variable modifications (listed by mass in Da) with modified residue and location within the peptide

Observed Modifications modifications from Delta Mass values as mapped to Unimod entries

Number of Phospho Sites count of phosphorylation sites within the peptide

Phospho Site Localization location and probability of phosphorylation site(s) within the peptide

Is Unique whether the identified sequence maps to a single identified protein (FALSE if shared between multiple proteins identified in the experiment)

Protein protein sequence header

Protein ID Protein identifier (primary accession number)

Entry Name protein entry name

Gene gene name

Protein Description protein name

Mapped Genes additional genes the peptide may originate from

Mapped Proteins additional proteins the peptide may originate from

Is Used whether the PSM is used in protein quantification

Purity precursor ion purity

(additional columns for TMT/iTRAQ experiments, each contains relative reporter ion abundances)