From e9f6a956854f7810358dc072e1443340149442f4 Mon Sep 17 00:00:00 2001
From: Fengchao <fcyucn@gmail.com>
Date: Sat, 16 Dec 2023 17:32:37 -0500
Subject: [PATCH] Update the commands for the new version.

---
 README.md | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a7172a3..6c8dc29 100644
--- a/README.md
+++ b/README.md
@@ -45,6 +45,13 @@ Usage:
         java -jar IonQuant.jar <options> --filelist <path to filelist file>
 Options:
         --specdir <string>     # Directory containing the spectral files (d/mzml/mzxml/raw/quantindex). One --specdir indicates one spectral directory and can have multiple --specdir.
+        --perform-ms1quant 0/1 # Perform MS1 quantification. 0 = no, 1 = yes. Default: 1
+        --perform-isoquant 0/1 # Perform isobaric labeling quantification. 0 = no, 1 = yes. Default: 0
+        --isotol <float>       # MS2 tolerance in ppm. Default: 10
+        --isolevel <int>       # Isobaric quantification level. 2 = MS2, 3 = MS3. Default: 2
+        --isotype <string>     # Isobaric quantification type. Case insensitive. Support iTRAQ-4, iTRAQ-8, TMT-0, TMT-2, TMT-6, TMT-10, TMT-11, TMT-16, TMT-18, sCLIP-6, iBT-16. Default: TMT-10
+        --annotation <string>  # Annotation file info for the isobaric quantification. Format: <path to psm.tsv>=<path to annotation file>. One --annotation indicates one annotation file and can have multiple --annotation. Default: <blank>
+        --site-reports 0/1     # Generate site reports. 0 = no, 1 = yes. The psm.tsv need to have the modification localization modification columns. Default: 1
         --threads <integer>    # Number of threads. 0 = all logical cores. Default: 0
         --mztol <float>        # MS1 tolerance in PPM. Default: 10.0
         --imtol <float>        # 1/K0 tolerance. Default: 0.05
@@ -76,7 +83,7 @@ Options:
         --requantify 0/1       # Re-quantify unidentified feature based on identified feature. Only activate when --light, --medium, or --heavy is not empty. Default: 1
         --writeindex 0/1       # Write indexed file on disk for further usage. 0 = no, 1 = yes. Default: 0
         --locprob <float>      # Localization probability threshold. Default: 0
-        --filelist <string>    # A file containing --specdir, and --psm. Default: <blank>
+        --filelist <string>    # A file containing flags. Default: <blank>
         --uniqueness 0/1/2     # Peptide-protein uniqueness. 0 = unique+razor, 1 = unique only, 2 = all. Default: 0
         --modlist <string>     # A file lists modification masses. Those masses are used to remove the mass discrepancy due to rounding errors. Default: <blank>
 ```