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PSM reports
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 variable 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
UniProt 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)