Introduction

The following sections will give you an overview of pyXLMS and get you familiar with using pyXLMS as a python package. It is assumed that pyXLMS is already installed on your system at this point, if not please refer to ➡️ Installation!

Abbreviations

The following abbreviations are commonly used throughout the documentation:

CSMs: Crosslink-Spectrum-Matches ➡️ Crosslink associated with a specific mass spectrum.
XLs: Crosslinks/residue pairs (the two terms are used interchangeably) ➡️ Two specific protein residues that are connected via a crosslinker.
FDR: False-Discovery-Rate ➡️ Commonly used quality metric in proteomics.

Following Along

Most of the following pages are based on Jupyter notebooks which are available from here .

You can follow along via the following steps:

Install JupyterLab


pip install jupyterlab

Clone the pyXLMS Repository


git clone --depth 1 https://github.com/hgb-bin-proteomics/pyXLMS.git

Change to the pyXLMS Directory


cd pyXLMS

Launch JupyterLab


jupyter lab

Run Example Notebooks

Navigate to the notebook you want to run in the JupyterLab file browser and open it.
Execute the cells from top to bottom.

Introductory Content

The Working with pyXLMS section will introduce you to the supported crosslink search engines and input formats [page] as well as supported output formats and down-stream analysis tools [page]. Moreover it will give an overview on how pyXLMS stores and encodes data as well as how to access that data [page]. The pyXLMS specific file format for CSMs and XLs will also be introduced here [page]. Finally, the section closes with instructions on how to create CSMs and XLs [page].

Tip

We recommend reading through the whole Working with pyXLMS section which will make understanding of subsequent sections substantially easier!