Ion reports

Column contents of the ion.tsv output file are described below:

Peptide Sequence peptide amino acid sequence, no modifications included

Modified Sequence peptide sequence including variable modifications

Peptide Length number of residues in the peptide sequence

M/Z calculated mass-to-charge ratio of the peptide

Charge peptide ion charge state

Observed Mass calculated peptide mass (in Da)

Probability confidence score determined by PeptideProphet

Expectation expectation value from statistical modeling with PeptideProphet

Spectral Count number of corresponding PSMs

Intensity peptide ion abundance

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

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

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