From ce0549614da22d619f79a8538e72bae59992f36c Mon Sep 17 00:00:00 2001 From: Vadim Demichev <30595084+vdemichev@users.noreply.github.com> Date: Tue, 26 Nov 2024 11:54:08 +0100 Subject: [PATCH] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index edc20be..9b51f39 100644 --- a/README.md +++ b/README.md @@ -412,8 +412,8 @@ Note that --lib-fixed-mod is no longer necessary as the library generated in Ste * **Contaminants** Adds common contaminants from the Cambridge Centre for Proteomics (CCP) database and automatically excludes them from quantification, see the description of the --cont-quant-exclude option. This option applies when generating a predicted spectral library from a FASTA database or analysing using such a library, if it was generated with **Contaminants** enabled. **Precursor ion generation** pane -* **FASTA digest** instructs DIA-NN to in silico digest the sequence database, for library-free search or to generate a spectral library in silico -* **Deep learning-based spectra, RTs and IMs prediction** instructs DIA-NN to perform deep learning-based prediction of spectra, retention times and ion mobility values. This allows not only to make in silico spectral libraries from sequence databases, but also to replace spectra/RTs/IMs in existing libraries with predicted values +* **FASTA digest** instructs DIA-NN to in silico digest the sequence database, for library-free search or to generate a spectral library in silico. +* **Deep learning-based spectra, RTs and IMs prediction** instructs DIA-NN to perform deep learning-based prediction of spectra, retention times and ion mobility values. This allows not only to make in silico spectral libraries from sequence databases, but also to replace spectra/RTs/IMs in existing libraries with predicted values. This option must not be used together with raw data analysis, i.e. in silico predicted library generation must be done in a separate step. **Output** pane * **Use existing .quant files when available** reuse IDs/quantification information from a previous analysis, see [Output](#output)