Peptide Hydrophobicity
Estimate a peptide retention proxy from average hydropathy and caller calibration.
Description
A peptide retention proxy uses a linear calibration on mean hydropathy.
A peptide retention proxy uses a linear calibration on mean hydropathy. The calibration is supplied and can describe a particular experimental setup.1
Estimate a peptide retention proxy from average hydropathy and caller calibration.
When to use Peptide Hydrophobicity
Use this tool to estimate a peptide retention proxy from average hydropathy and caller calibration.
Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
How to use Peptide Hydrophobicity and understand its results
- Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
- Enter sequence, minutesPerHydropathyUnit, baseRetentionMinutes using the field table and calculation rules, then run the tool.
- Read meanHydropathy, retentionProxyMinutes. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| sequence | Sequence | string | Required |
| minutesPerHydropathyUnit | Minutes per hydropathy unit | number | Required |
| baseRetentionMinutes | Base retention minutes | number | Required |
Enter a canonical sequence and finite slope/intercept. Compute mean Kyte–Doolittle score and the linear retention proxy; negative slope, intercept or predicted time is allowed.
The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.
retentionMinutes=baseMinutes+meanHydropathy×minutesPerHydropathyUnit Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| meanHydropathy | Mean hydropathy | number |
| retentionProxyMinutes | Retention proxy minutes | number |
{
"input": {
"sequence": "AIL",
"minutesPerHydropathyUnit": 2,
"baseRetentionMinutes": 10
},
"output": {
"meanHydropathy": 3.3666666666666667,
"retentionProxyMinutes": 16.733333333333334
}
}Limitations and assumptions
No chromatographic fit, solvent gradient or instrument calibration is performed. The output is a proxy that requires independently validated calibration.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Protein GRAVY: Compute grand average of Kyte–Doolittle hydropathy. For a complementary task, use Transmembrane Window Scan: Detect transmembrane helix candidates from local hydropathy windows.
References
-
Peptide Hydrophobicity — tool.io
Similar or alternative tools
- Protein GRAVY
Compute grand average of Kyte–Doolittle hydropathy.
- Transmembrane Window Scan
Detect transmembrane helix candidates from local hydropathy windows.