From 963d9de102f637a3df04c96ffd535d7a17717468 Mon Sep 17 00:00:00 2001 From: ypriverol Date: Thu, 25 Nov 2021 12:00:16 +0000 Subject: [PATCH] docs --- docs/identification.rst | 9 +++++++++ docs/index.rst | 4 ++++ 2 files changed, 13 insertions(+) diff --git a/docs/identification.rst b/docs/identification.rst index 1fa31d68..63dba410 100644 --- a/docs/identification.rst +++ b/docs/identification.rst @@ -35,9 +35,18 @@ The RAW data (files from the instrument) can be provided to quantms pipeline in Additionally to file conversion, the Raw conversion step allows the users to perform an extra peak-picking step ```openmspeakpicker true``` for those datasets/projects where peaks can be extracted using the Thermo RAW API. Read more about the OpenMS peak picker algorithm `here `_ . +Target/Decoy database generation +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Target/Decoy is the most common approach to control the number of false positive peptides and proteins identified by the corresponding workflow [ref 3]. The user can provide the protein FSATA database with the decoys already attached or generate the database within the pipeline by using the following option: ```add_decoys```. + +.. hint:: Additionally, the user can define the prefix for the decoy proteins (e.g. DECOY_) by using the parameter ```decoy_string```. We STRONGLY recommend to use DECOY_ prefix for all the decoy proteins for better compatibility with exiting tools such as :doc:`pquant` or :doc:`pmultiqc` + References --------------------- [1] Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA. Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):63-76. doi: 10.1016/j.bbapap.2013.02.032. Epub 2013 Mar 1. PMID: 23467006; PMCID: PMC3898926. [2] Perez-Riverol Y, Moreno P. Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines. Proteomics. 2020 May;20(9):e1900147. doi: 10.1002/pmic.201900147. Epub 2019 Dec 18. PMID: 31657527. +[3] Elias JE, Gygi SP. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol. 2010;604:55-71. doi: 10.1007/978-1-60761-444-9_5. PMID: 20013364; PMCID: PMC2922680. + diff --git a/docs/index.rst b/docs/index.rst index fef05d60..7c70c2f9 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -13,6 +13,10 @@ Contents .. toctree:: :maxdepth: 2 + identification + .. toctree:: + :maxdepth: 2 +