FindPept
Match experimental masses to theoretical protein digest fragments for peptide mass fingerprinting.
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What is FindPept?
FindPept matches a list of experimental peptide masses from mass spectrometry against the theoretical digest fragments of a protein sequence. This technique, known as peptide mass fingerprinting (PMF), identifies which observed peaks in a mass spectrum correspond to specific segments of a known protein. FindPept supports configurable enzyme, mass type, tolerance, and missed cleavage parameters, making it suitable for a range of PMF workflows in proteomics research.
Where the related Peptide mass calculator generates a complete theoretical digest with masses, FindPept works in the opposite direction: starting from experimental masses and asking "which peptide fragments do these masses correspond to?" The two tools complement each other -- Peptide mass for planning digestion experiments, FindPept for interpreting mass spectrometry results.
How to use FindPept online
ProteinIQ runs FindPept entirely in the browser with instant results -- no server round-trip or account required.
Input
| Input | Description |
|---|---|
Protein sequence | A single protein sequence in FASTA format (pasted, uploaded as .fasta/.txt/.pdb, or fetched by PDB ID from RCSB). PDB files are automatically converted to FASTA. |
Experimental masses | A list of observed peptide masses (in Daltons) separated by commas, spaces, or newlines. |
Settings
| Setting | Default | Description |
|---|---|---|
Enzyme | Trypsin | The protease used for digestion. Options: Trypsin, Chymotrypsin, Pepsin (pH 1.3), or None (treats the entire sequence as a single fragment). |
Mass type | Monoisotopic | Monoisotopic uses the most abundant isotope for each element (higher precision, standard for modern instruments). Average uses the natural isotope distribution average (appropriate for lower-resolution data). |
Mass tolerance | 0.5 Da | Maximum allowed difference between an experimental mass and a theoretical fragment mass for a match. Range: 0.01 -- 2.0 Da in 0.01 Da steps. |
Max missed cleavages | 1 | Number of internal enzyme cleavage sites that may remain uncleaved in a single fragment. Range: 0 -- 3. Higher values generate more candidate fragments but increase the chance of spurious matches. |
Output
Each row represents a match between one experimental mass and one theoretical digest fragment.
| Column | Description |
|---|---|
Experimental mass | The input mass value (Da) that was matched. |
Theoretical mass | The calculated mass of the matching peptide fragment (Da). |
Mass difference | Experimental minus theoretical mass (Da). Positive values indicate the experimental mass is heavier. |
Peptide sequence | The amino acid sequence of the matched fragment. |
Position | Start and end residue numbers (1-based) within the protein sequence. |
Missed cleavages | Number of internal enzyme cleavage sites contained within this fragment. |
Summary statistics are displayed above the table: total theoretical fragments generated, number of matched masses, number of unmatched masses, and sequence coverage percentage.
Results can be downloaded as CSV or JSON.
How FindPept works
The algorithm proceeds in three steps:
-
Theoretical digest: The protein sequence is cleaved in silico using the selected enzyme's specificity rules. For trypsin, cleavage occurs after K and R (blocked by P at P1'). Fragments with up to the specified number of missed cleavages are generated by combining adjacent peptides across uncleaved sites.
-
Mass calculation: Each theoretical fragment's mass is computed by summing residue masses (monoisotopic or average) and adding the water molecule mass (18.01056 Da monoisotopic / 18.01524 Da average) for the peptide bond termini.
-
Mass matching: Every experimental mass is compared against every theoretical fragment mass. If the absolute difference falls within the tolerance window, the pair is recorded as a match. A single experimental mass may match multiple fragments (e.g., when two peptides have similar masses), and a single fragment may be matched by multiple experimental masses.
Sequence coverage is calculated as the percentage of residue positions in the protein that are covered by at least one matched fragment.
Applications
- Mass spectrometry data interpretation: After acquiring a MALDI-TOF or ESI mass spectrum of a protein digest, use FindPept to identify which peaks correspond to expected tryptic (or other enzyme) fragments. This confirms protein identity and highlights post-translational modifications when observed masses deviate from theoretical values.
- Protein identification by PMF: Peptide mass fingerprinting remains a rapid first-pass identification method. By matching experimental masses to a known protein sequence, researchers can confirm that the correct protein was expressed, purified, or immunoprecipitated.
- Quality control of recombinant proteins: Verify that a purified recombinant protein has the expected sequence by checking that the digest mass fingerprint matches. Unmatched masses may indicate truncations, mutations, or modifications.
- Missed cleavage analysis: Adjusting the missed cleavage parameter reveals whether incomplete digestion is producing larger-than-expected fragments, which helps optimize digestion conditions.
Limitations
- Single protein only: FindPept matches masses against one protein sequence at a time. For database-wide PMF searches across entire proteomes, dedicated tools like Mascot or MS-Fit are more appropriate.
- No modification support: The current implementation does not account for post-translational modifications (phosphorylation, oxidation, etc.) or chemical adducts. Modified peptides will appear as unmatched masses or may spuriously match a different fragment within tolerance.
- Primary sequence only: Theoretical digestion is based on amino acid sequence rules and does not consider whether cleavage sites are sterically accessible in the folded protein.
- Tolerance in Daltons only: The tolerance window is specified in absolute Daltons. Parts-per-million (ppm) tolerance, which is more appropriate for high-resolution instruments, is not exposed in the current interface.