FindPept

How to match peptide masses to a protein sequence

Paste one protein sequence and a list of neutral peptide masses in Da, choose the digestion enzyme, and click Match Masses. FindPept compares those observations with unmodified theoretical digest fragments. The Results table lists every candidate match; Summary reports matched and unmatched masses, fragment count, and candidate sequence coverage. Calculations run in your browser.

Worked example: angiotensin II

Use this eight-residue peptide sequence:

>Angiotensin_II
DRVYIHPF

Paste these experimental masses:

289.13861
774.40646
1045.53451
1500

Keep the defaults: Enzyme = Trypsin, Mass type = Monoisotopic, Mass tolerance = 0.5, and Max missed cleavages = 1. The Results table contains:

Summary shows three matched masses, one unmatched mass (1500 Da), three candidate matches, and 100.0% coverage. The full-length match requires one missed cleavage. Displayed masses and differences are rounded independently to four decimal places; matching uses the unrounded numbers.

Input

Supply only mass values. Export the mass column from a peak table first: numeric intensity, charge, retention-time, or index columns would otherwise be interpreted as additional masses. Use a decimal point, without thousands separators. Do not paste units after individual values. Invalid values cause an error rather than being silently discarded.

Lowercase sequences, whitespace, invisible formatting characters, and position numbers separated from residues at line boundaries are handled. Put names and descriptions after > in a FASTA header, never on an unmarked line above the sequence. For example, a plain GFP line consists of valid amino acid letters and would be part of the sequence.

Gaps, stop markers, embedded numbers, modification annotations, and residues without a defined mass are rejected. Multiple FASTA records are rejected: run each protein separately. PDB input is converted to sequence and reported with a warning; submit one protein chain. Coordinate-derived sequences can omit unresolved residues, so use the complete protein FASTA sequence for digest interpretation.

Neutral mass versus m/z

FindPept uses unmodified neutral mass [M], not the mass-to-charge ratio of an ion. For a positively protonated ion with charge $z$, convert using $M = z(m/z) - z m_p$, where the proton mass is approximately $1.00728$ Da. For a singly charged [M+H]+ peak, subtract one proton mass before entering it. This conversion does not handle sodium adducts or peptide modifications.

Use the Peptide mass calculator when you need masses for ion types or supported chemical modifications.

Settings

Results and interpretation

Results are ordered by experimental mass, then sequence start position. Copy or download the table using its controls. The Summary tab contains the protein identifier and length, calculation settings, fragment count, matched and unmatched observation counts, candidate match count, coverage, and the full unmatched mass list. Summary can also be copied or downloaded.

A single experimental mass can match several positions. For AKAK, the neutral monoisotopic mass 217.14263 Da matches AK at positions 1-2 and 3-4: one matched mass, two candidate matches, and 100.0% candidate coverage. Duplicate input masses remain separate observations. Coverage counts each residue position once across all candidate matches, including ambiguous matches.

A run with no matches still provides a Summary and a warning. Before increasing tolerance, check neutral mass conversion, mass type, enzyme, and sample modifications. A close mass match or high coverage alone does not establish protein identity or distinguish isobaric sequences.

Calculation method and scope

The tool generates enzyme-specific fragments using the same cleavage rules as Peptide Cutter, then combines adjacent fragments up to the missed-cleavage setting. Trypsin cuts after K or R unless followed by P. The current Chymotrypsin option cuts after F, Y, W, M, or L unless followed by P; the Pepsin option uses a simplified cut-after-F/L rule. These sequence rules do not model experimental digestion efficiency or accessibility.

Each neutral mass is the sum of the fragment's residue masses plus one water molecule for its termini. Water contributes 18.01056 Da in monoisotopic mode and 18.01528 Da in average mode. A match is recorded when the absolute experimental-minus-theoretical difference is at most the chosen tolerance.

ProteinIQ's FindPept searches digest fragments of one supplied protein. It does not search a protein database, identify modifications, or test enzyme autolysis. It also does not enumerate arbitrary subsequences: None means the intact sequence. The ExPASy FindPept service has a broader purpose, including unspecific cleavage and modification analysis. ProteinIQ's calculation is not a reproduction of all its features.

Common questions

Why do my MALDI or ESI peaks have no matches?

Check whether the exported values are neutral masses or m/z. Protonated peaks, chemical modifications, contaminating proteins, and an incorrect digestion setting can all produce unmatched observations. FindPept cannot identify the cause from an unmatched mass alone.

Can a mass match more than one peptide?

Yes. Every fragment within the tolerance window is retained. The match list is a set of candidates, not a ranked identification or statistical confidence score.

Can I upload a mass and intensity table?

Extract its mass column first. FindPept accepts mass-only numeric lists and one-column CSV or TSV data; it does not infer which numeric column represents mass.

References

• ExPASy mass values and UniMod mass values document residue and atomic masses used for peptide calculations.
• ExPASy PeptideMass documentation explains theoretical digestion, mass conventions, and modifications.
• Gattiker et al., 2002 describes the broader ExPASy FindPept method for unmatched masses.