diff --git a/README.md b/README.md index e17fa17..6dbf5ff 100644 --- a/README.md +++ b/README.md @@ -186,19 +186,19 @@ Internally generated decoys will have protein accessions matching "{decoy_tag}{a "C": 57.0215 // Apply static modification to cysteine }, "variable_mods": { // Optional[Dict[char, float]] {default={}}, variable modifications - "M": 15.9949 // Variable mods are applied *before* static mods - "$": 49.2022 // Apply variable modification to C-terminus of peptide - "[": 42.0 // Apply variable modification to N-terminus of protein + "M": 15.9949, // Variable mods are applied *before* static mods + "$": 49.2022, // Apply variable modification to C-terminus of peptide + "[": 42.0, // Apply variable modification to N-terminus of protein "]": 111.0 // Apply variable modification to C-terminus of protein }, "max_variable_mods": 2, // Optional[int] {default=2} Limit k-combinations of variable modifications "decoy_tag": "rev_", // Optional[str] {default="rev_"}: See notes above - "generate_decoys": false // Optional[bool] {default="true"}: Ignore decoys in FASTA database matching `decoy_tag` + "generate_decoys": false, // Optional[bool] {default="true"}: Ignore decoys in FASTA database matching `decoy_tag` "fasta": "dual.fasta" // str: mandatory path to FASTA file }, "quant": { // Optional - specify only if TMT or LFQ "tmt": "Tmt16", // Optional[str] {default=null}, one of "Tmt6", "Tmt10", "Tmt11", "Tmt16", or "Tmt18" - "lfq": true, // Optional[bool] {default=null}, perform label-free quantification + "lfq": true // Optional[bool] {default=null}, perform label-free quantification }, "precursor_tol": { // Tolerance can be either "ppm" or "da" "da": [