A residue sequence is only part of a peptide’s description when terminal groups, labels or other modifications are present. A publication should identify those features clearly enough that another researcher does not mistake a different molecular form for the material used.
Describe what the modification changes in the record
The ProForma 2.0 standards paper describes a notation for modified peptide and protein forms, including terminal modifications, cross-links and ambiguity in modification position. Its purpose illustrates the need to encode more than an unannotated amino-acid string.LeDuc and colleagues — ProForma 2.0: Unifying the encoding of proteoforms and peptidoforms (opens in a new tab)
In a methods description, name each relevant terminal group or residue modification and its location. “Labelled peptide” is incomplete if several attachment positions or linker arrangements are possible.
Keep the description tied to the construct actually used. A general discussion of a modification’s possible biological effects does not replace a precise material definition.
Report the evidence level as well: intended synthesis design, supplier declaration and experimental assignment are different bases for a structural statement.
Separate molecular features from supplied components
| Feature | Detail needed |
|---|---|
| N- and C-termini | State each terminal group explicitly |
| Residue modification | Name the modification and identify its position |
| Label or conjugate | Describe attachment site and any linker |
| Cyclisation or cross-link | Identify the linked sites and linkage type where known |
| Counterion or formulation | Report separately with its documentary basis |
For an illustrative short chain, an N-terminal acetyl group and a C-terminal amide should not be collapsed into the word “modified”. Readers need to know which end carries which feature.
Similarly, a salt designation should not be inserted into the residue sequence as though it were an additional amino acid. The complete supplied material can include components that require separate reporting fields.
A drawing can clarify a complex connection, but the accompanying text should identify the notation and explain any unresolved position. A neat structure image must not imply more certainty than the evidence supports.
Report ambiguous assignments explicitly
If an analysis supports a modification but not its exact location, state the supported assignment and the remaining positional ambiguity. Do not choose the most convenient site merely to produce a single clean sequence string.
If a supplier gives a trade name without the underlying modification description, preserve that limitation. A name shared with a publication does not establish that both sources refer to the same molecular form.
Keep measured and calculated masses labelled separately where they are reported. A mass agreement can be relevant without resolving every positional or stereochemical alternative.
Keep all representations aligned
Compare the text description, sequence annotation, structure drawing and supplementary metadata before submission. They should describe compatible molecular forms and preserve the same uncertainties.
If a journal requests a particular format, follow its current instructions while retaining a clear human-readable description. A machine-readable string is useful only when its syntax and definitions are available to the reader.
The reporting aim is a complete, appropriately qualified identity statement. It does not require claiming that every modification was independently located when the study did not generate that evidence.
Sources and further detail
- LeDuc and colleagues — ProForma 2.0: Unifying the encoding of proteoforms and peptidoforms (opens in a new tab)
Original standards-paper abstract checked for terminal modifications, cross-links and positional ambiguity. Cited as the 2.0 paper, not a claim that 2.0 is the latest specification; HUPO-PSI lists 2.1 final in June 2026.
Sources checked 20 September 2026. Reporting examples are illustrative unless explicitly identified as supplied-document transcriptions. This article has not undergone independent scientific peer review.