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X!TandemPipeline User Manual
X!TandemPipeline User Manual
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###### X!TandemPipeline 0.4.51

# X!TandemPipeline User Manual

## Free and Open Source Protein Identification Software

Authors: Benoît Valot, Olivier Langella, Thomas Renne, Filippo Rusconi, and Michel Zivy
Publication Date: February 09, 2022 , Version: 0.4.51

# Dedication

To all the admirable people acting in the “Free Software Movement” for a better and more ethical computing world

To all the readers who helped with this manual.

2.1 Peptidic Bond Formation by Condensation
2.2 End Capping Chemistry of the Protein Polymer
2.3 Protein Cleavage by Water and Cyanogen Bromide
2.4 Protein fragmentation patterns most widely encountered
2.5 Theoretical and experimental parallel data-producing processes
2.6 The steps leading to a scored peptide vs mass spectrum match (PSM)
2.7 Computation of a peptidic expectation value (E-value)
2.8 Protein inference: constructing a consolidated protein identifications list
2.9 Phospho-site inference: constructing a consolidated phospho-site list
3.1 Main program window
3.2 X﻿!﻿Tandem-based identification configuration
3.3 X﻿!﻿Tandem presets configuration window (Spectrum tab)
3.4 X﻿!﻿Tandem run feedback to the user
3.5 X﻿!﻿Tandem run finished message to the user
3.6 Configuration of the loading of the identification results
3.7 Selecting a particular identification results file's data set
3.8 Selecting a particular identification results file's data set
3.9 Displaying the MS identifications list (first columns)
3.10 Displaying the MS identifications list (last columns)
4.1 The protein list window
4.2 Protein identification filter parameters tab of the main window
4.3 False discovery rate (FDR) data after a protein inference process is run
4.4 Mass precision quality assessment
4.5 Protein details window
4.6 The peptide list window (first columns)
4.7 Peptide list window (last columns)
4.8 Columns that populate the peptide list table view
4.9 Peptide details window
4.10 The extracted ion current (XIC) chromatogram viewer window
4.11 The extracted ion current (XIC) chromatogram viewer window (zoomed view)
5.1 X﻿!﻿Tandem settings window for a phospho-proteomics project
5.2 Setting the project to be a phospho-proteomics project
5.3 Configuring the phosphorylated residues
5.4 The main window's Identifications tab
5.5 PTM islands list window
5.6 Protein details window
5.7 PTM peptides list window (first columns)
5.8 PTM peptides list window (last columns)
5.9 Peptide details window
5.10 Two mass spectrum vs peptide matches (PSM) in a single MS/MS scan
5.11 The extracted ion current (XIC) chromatogram viewer window
6.1 The Edit menu showing various configuration tasks
6.2 Modifications editor window (folded)
6.3 Modifications editor window (unfolded)
6.4 PSI MOD selection window
6.5 Labeling methods editor window
6.6 Chemical modifications are tagged with their PSI-MOD code
6.7 General settings window
7.1 Defining sample associations for XIC alignments
7.2 Sample associations are done by grouping samples into groups
7.3 Setting the reference sample for the alignment
7.4 The MassChroQ interface window (Sample associations)
7.5 The MassChroQ interface window (Sample associations) - all samples listes
7.6 The MassChroQ interface window (Sample associations) - pre-defined sample associations
7.7 The MassChroQ interface window (Alignment)
7.8 The MassChroQ interface window (peak quantification)
7.9 The MassChroQ interface window (MassChroQ)
7.10 Contents of the masschroqml file

Copyright 2021,2022 Filippo Rusconi and Olivier Langella

Thierry Balliau and Marlène Davanture are warmly thanked for their outstanding technical help while writing this user manual.

X﻿!﻿TandemPipeline

http://pappso.inrae.fr/en/bioinfo/xtandempipeline/

This book is part of the X﻿!﻿TandemPipeline project.

The X﻿!﻿TandemPipeline project is the successor of the Java language-based homonymous project. This project is a full rewrite of the former project in the C++ language, with many new features added.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org.

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