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\section{Getting started}

\subsection{Data conversion}
\label{Data_Conversion}

Each MS instrument vendor has one or more formats for storing the acquired data. Converting these data into an open format (preferably mzML) is the very first step when you want to work with open-source mass spectrometry software. A freely available conversion tool is ProteoWizard. The OpenMS installation package for Windows automatically installs ProteoWizard, so you do not need to download and install it separately.

Please note that due to restrictions from the instrument vendors, file format conversion for most formats is only possible on Windows systems, so exporting from the acquisition PC connected to the instrument is usually the most convenient option.
All files used in this tutorial have already been converted to mzML by us, so you do not need to do it yourself.

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\section{Getting started}

Before we get started we will install OpenMS and KNIME using the installers provided on the USB stick. Please choose the directory that matches your operating system and execute the installer. Note that these steps are not be necessary if you use one of our laptops.

For example for Windows you call
\begin{itemize}
\item the OpenMS installer: \directory{Windows / OpenMS-2.0\_Win64\_setup.exe}
\item the KNIME installer: \directory{Windows / OpenMS-2.0-prerequisites-installer.exe} \\ and \directory{Windows / KNIME\ 2.12.0\ Installer\ (64bit).exe}
\end{itemize}

on Mac you call
\begin{itemize}
\item the OpenMS installer: \directory{Mac / OpenMS-2.0.0\_setup.dmg}
\item the KNIME installer: \directory{Mac / knime\_2.12.0.macosx.cocoa.x86\_64.dmg}
\end{itemize}

and follow the instructions.

\subsection{Data conversion}
\label{Data_Conversion}

Each MS instrument vendor has one or more formats for storing the acquired data. Converting these data into an open format (preferably mzML) is the very first step when you want to work with open-source mass spectrometry software. A freely available conversion tool is ProteoWizard. The OpenMS installation package for Windows automatically installs ProteoWizard, so you do not need to download and install it separately.

Please note that due to restrictions from the instrument vendors, file format conversion for most formats is only possible on Windows systems, so exporting from the acquisition PC connected to the instrument is usually the most convenient option.
All files used in this tutorial have already been converted to mzML by us, so you do not need to do it yourself.

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