Methionine Oxidation Screen
Screen exposed methionines as oxidation candidates, not measured modifications.
Description
A methionine-oxidation candidate screen combines residue identity with supplied accessibility.
A methionine-oxidation candidate screen combines residue identity with supplied accessibility. It does not infer accessibility from sequence.1
Screen exposed methionines as oxidation candidates, not measured modifications.
When to use Methionine Oxidation Screen
Use this tool to screen exposed methionines as oxidation candidates, not measured modifications.
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 Methionine Oxidation Screen 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, surfaceAccessibility, minimumAccessibility using the field table and calculation rules, then run the tool.
- Read exposedMethionineIndexes, methionineCount. 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 |
| surfaceAccessibility | Surface accessibility | list of number | Required |
| minimumAccessibility | Minimum accessibility | number | Required |
Enter canonical sequence, one accessibility fraction per normalized residue and minimum in 0–1. Return ascending zero-based exposed methionine indexes and total methionines.
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.
candidateIndexes={i:residue_i=M AND accessibility_i≥minimum} Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| exposedMethionineIndexes | Exposed methionine indexes | list of number |
| methionineCount | Methionine count | number |
{
"input": {
"sequence": "AMM",
"surfaceAccessibility": [
0,
0.8,
0.2
],
"minimumAccessibility": 0.5
},
"output": {
"exposedMethionineIndexes": [
1
],
"methionineCount": 2
}
}Limitations and assumptions
Threshold equality passes. Structure, oxidative conditions and measured modification occupancy are not assessed.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. 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 Phosphorylation Sites: Count potential Ser/Thr/Tyr phosphorylation positions. For a complementary task, use Deamidation Motifs: Locate N-G and Q-G deamidation-susceptibility sequence motifs.
References
-
Methionine Oxidation Screen — tool.io
Similar or alternative tools
- Phosphorylation Sites
Count potential Ser/Thr/Tyr phosphorylation positions.
- Deamidation Motifs
Locate N-G and Q-G deamidation-susceptibility sequence motifs.