Peptide reports

Column contents in the peptide.tsv output file are described below. Each row is an identified peptide sequence.

Peptide peptide amino acid sequence, no modifications included ('stripped' peptide sequence)

Peptide Length number of residues in the peptide sequence

Charges peptide ion charge state(s)

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

Spectral Count number of corresponding PSMs

Intensity relative abundance (peak intensity) of the precursor ion

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

Observed Modifications for peptides identified with non-zero delta masses (from open or mass offset searches), modifications mapping to a Unimod entry of the corresponding delta mass are listed here

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

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