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docs: remove mention of deleted parameters #160

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Nov 3, 2024
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docs: remove mention of deleted parameters #160

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8 changes: 1 addition & 7 deletions DOCS.md
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Expand Up @@ -164,8 +164,6 @@ For additional information about configuration options and output file formats,
"c_terminal": false, // Optional[bool] {default=true}. Cleave at c terminus of matching amino acid
"semi_enzymatic": false // Optional[bool] {default=false}. Generate semi-enzymatic peptides
},
"fragment_min_mz": 200.0, // Optional[float] {default=150.0}, Minimum mass of fragments to search
"fragment_max_mz": 2000.0, // Optional[float] {default=2000.0}, Maximum mass of fragments to search
"peptide_min_mass": 500.0, // Optional[float] {default=500.0}, Minimum monoisotopic mass of peptides to fragment
"peptide_max_mass": 5000.0, // Optional[float] {default=5000.0}, Maximum monoisotopic mass of peptides to fragment
"ion_kinds": ["b", "y"], // Optional[List[str]] {default=["b","y"]} Which fragment ions to generate and search?
Expand Down Expand Up @@ -291,8 +289,6 @@ Example:

### Fragment Settings

- **fragment_min_mz**: Float. The minimum mass of fragments to search (default: 150.0).
- **fragment_max_mz**: Float. The maximum mass of fragments to search (default: 2000.0).
- **peptide_min_mass**: Float. The minimum monoisotopic mass of peptides to fragment *in silico* (default: 500.0).
- **peptide_max_mass**: Float. The maximum monoisotopic mass of peptides to fragment *in silico* (default: 5000.0).
- **ion_kinds**: List of strings. Which fragment ions to produce? Allowed values: "a", "b", "c", "x", "y", "z". (default: ["b", "y"])
Expand All @@ -301,8 +297,6 @@ Example:
Example:
```json
"database": {
"fragment_min_mz": 150.0,
"fragment_max_mz": 2000.0,
"peptide_min_mass": 500.0,
"peptide_max_mass": 5000.0,
"ion_kinds": ["b", "y"],
Expand Down Expand Up @@ -501,4 +495,4 @@ The "results.sage.tsv" file contains the following columns (headers):
- `ms1_intensity`: Intensity of the selected MS1 precursor ion (not label-free quant)
- `ms2_intensity`: Total intensity of MS2 spectrum

These columns provide comprehensive information about each candidate peptide spectrum match (PSM) identified by the Sage search engine.
These columns provide comprehensive information about each candidate peptide spectrum match (PSM) identified by the Sage search engine.
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