Peptidoform¶

A peptidoform is a specific molecular form of a peptide: the amino acid sequence together with all of its modifications. In QPX, peptidoforms are encoded using the ProForma notation, which provides a standardized, human-readable string representation for modified peptide sequences.

The peptidoform field appears alongside the bare sequence field (amino acids only) in every identification- and quantification-level view. While sequence gives the unmodified backbone, peptidoform captures the complete molecular identity needed to distinguish different modified forms of the same peptide.

ProForma notation¶

ProForma is a HUPO-PSI standard for encoding peptide sequences with modifications in a single string. Modifications are placed in square brackets immediately after the residue they modify (or before the sequence for N-terminal modifications).

Examples¶

Basic modification by name

PEPTIDM[Oxidation]K

Methionine at position 7 carries an Oxidation modification.

Modification by UNIMOD accession (recommended)

PEPTIDM[UNIMOD:35]K

Same as above, but using the UNIMOD accession number. This is the recommended approach because accessions are unambiguous.

N-terminal modification

[Acetyl]-PEPTIDMK

Acetylation on the N-terminus of the peptide.

Multiple modifications

[Acetyl]-PEPT[Phospho]IDM[Oxidation]K

N-terminal acetylation, phosphorylation on threonine at position 4, and oxidation on methionine at position 7.

TMT-labeled peptide

[TMT6plex]-PEPTIDM[Oxidation]K[TMT6plex]

TMT6plex isobaric tag on the N-terminus and on the C-terminal lysine, with an additional oxidation on methionine.

Tip

When a modification does not have a UNIMOD entry, use the CHEMMOD notation to specify the mass shift in Daltons: PEPTIDM[CHEMMOD:+15.9949]K.

Where peptidoform is used¶

The peptidoform field is present in the following QPX views:

View	Field name	Description
PSM (`psm_file`)	`peptidoform`	The identified peptidoform for this spectrum match
Feature (`feature_file`)	`peptidoform`	The quantified peptidoform for this feature
Peptide (`peptide_file`)	`peptidoform`	The peptidoform summarized across samples

In all three views, the peptidoform string serves as a key component of the record identity alongside charge and run_file_name.

Relationship to the modifications field¶

The peptidoform string encodes modifications inline, which is compact and human-readable. However, some use cases require structured access to modification details -- for example, querying all phosphorylation sites with their localization probabilities.

For this purpose, QPX provides a separate modifications field that represents the same information as a structured array of records. See the Modifications page for the full struct definition and examples.

Warning

The peptidoform string and the modifications struct should be consistent with each other. If both are present, consumers should treat the peptidoform as the canonical representation and the modifications field as supplementary detail.