PSM reports

psm.tsv column contents are described below:

Spectrum MS/MS spectrum identifier, follows the format (file name).(scan #).(scan #).(charge)

Spectrum File name of originating identification file

Peptide peptide amino acid sequence, any modifications not included ('stripped' peptide sequence)

Modified Peptide peptide sequence including modifications, modified residues are followed by brackets containing the integer mass (in Da) of the residue plus the modification; blank if peptide is unmodified

Peptide Length number of residues in the peptide sequence

Charge charge state of the identified peptide

Retention retention time (in seconds)

Observed Mass mass of the identified peptide (in Da)

Calibrated Observed Mass mass of the identified peptide after m/z 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 m/z 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 (in Da)

Expectation expectation value from statistical modeling with PeptideProphet, lower values indicate higher likelihood

Hyperscore similarity score between observed and theoretical spectra, higher values indicate greater similarity

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

PeptideProphet Probability confidence score determined by PeptideProphet, higher values indicate greater confidence

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 (peak intensity) 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 (calculated by PTMProphet) 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 corresponding to the identified peptide sequence; this will be the selected razor protein if the peptide maps to multiple proteins (in this case, other mapped proteins are listed in the 'Mapped Proteins' column)

Protein ID protein identifier (primary accession number) for the selected protein

Entry Name entry name for the selected protein

Gene gene name for the selected protein

Protein Description name of the selected protein

Mapped Genes additional genes the identified peptide may originate from

Mapped Proteins additional proteins the identified peptide maps to

Is Used whether the PSM is used in protein quantification ('TRUE' means this PSM's intensity contributes to protein abundance)

Purity Precurson ion intensity as a percentage of total ion intensity in the MS1 scan.

(additional columns for TMT/iTRAQ channels, where each contains the relative reporter ion abundances for that PSM)