From 9c500d81e895547f21bc710c3d977fd3564cd803 Mon Sep 17 00:00:00 2001 From: Grigory Reznikov Date: Wed, 15 Apr 2026 18:42:58 +0200 Subject: [PATCH] Add documentation for combine_charge_states and peptide_q_value options --- DOCS.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/DOCS.md b/DOCS.md index b186bf03..98ca7c21 100644 --- a/DOCS.md +++ b/DOCS.md @@ -200,7 +200,8 @@ For additional information about configuration options and output file formats, "ppm_tolerance": 5.0, // Optional[float] {default = 5.0}, tolerance (in p.p.m.) for DICE window around calculated precursor mass // Optional[bool] {default = true}. Combine all charge states for quantification. Setting this to false // quantifies each peptide-charge precursor in `precursor_charge` range (see below) separately - "combine_charge_states": true + "combine_charge_states": true, + "peptide_q_value": 0.01 // Optional[float] {default = 0.01}, maximum peptide-level q-value for reporting quantification results } }, "precursor_tol": { // Tolerance can be either "ppm" or "da" @@ -367,6 +368,8 @@ The quant section is optional and should be specified only if TMT or LFQ is used - **integration**: String. The method used for integrating peak intensities, either "Sum" or "Max" (default: "Sum"). - **spectral_angle**: Float. Threshold for the spectral angle similarity measure, ranging from 0 to 1 (default: 0.7). - **ppm_tolerance**: Float. Tolerance for matching MS1 ions in parts per million (default: 5.0). + - **combine_charge_states**: Boolean. If true, combine all charge states for quantification. If false, quantify each peptide-charge precursor separately (default: true). + - **peptide_q_value**: Float. Maximum peptide-level q-value for reporting quantification results (default: 0.01). Example: ```json