Ion reports

ion.tsv column contents are described below. Each row represents a peptide sequence identified in a certain charge and modification state.

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

Modified Sequence 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

M/Z calculated (theoretical) peptide mass-to-charge ratio based on identified sequence and modifications Charge peptide ion charge state

Observed Mass calculated mass of the identified peptide (in Da)

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

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

Spectral Count number of corresponding PSMs

Intensity peptide ion abundance

Assigned Modifications variable modifications (listed by modification 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 UniProt protein identifier (primary accession number)

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)