xiSEARCH: step by step instructions

Pre-requirements:

Installation:

  1. Download the ZIP file from http://xi3.bio.ed.ac.uk/downloads/xiSEARCH/.
  2. Extract the compressed files to your computer (e.g. C:\Users\John). You will have a new folder (C:\Users\John\xiSEARCH).

Running xiSEARCH

A short rundown of the usage can be found here.
  1. If you are using Windows start the startXiWindows file. If you are using Unix start the startXiUnix file. This will start Xi with a simple graphical user interface (GUI), and the actual java library (xiSEARCH.jar).
  2. The GUI has 5 tabs. In the first tab Run, choose the location where you want to save your results under the box result. Optional: In peak annotations you can define a file for writing out full annotations of the spectra.

  3. In the second tab Peak Lists select the peak lists to be searched (Supported formats: mgf-files as generated from msconvert or apl-files as produced by MaxQuant. For mgf-files of other sources the config may need to be adapted to define how to read out a run-name and a scan-number from the TITLE= tags in the files).

  4. In the third tab Fasta Files select the FASTA files to be searched. Load opens a file selection dialog. Multiple files can be selected there from the computer and one can be defined as custom decoy database by checking the appropriate box. If no decoy database is given, the program automatically generates one based on the target database. Xi does not run by default without decoy database.

  5. In the fourth tab Config the search is configured. All parameters are defined in form of a text file that can be edited in the GUI. The tab opens displaying a default config as an example that defines a search with BS3 as cross-linker, carboxyamidomethylation on cysteines as fixed modification, oxidation of methionine as variable modification and trypsin as the protease of choice. Additional options are still included with a short description of their function, example and the syntax. When you have your config file defined you can save it for further searches under the box Save. Load allows you to open saved config files from your computer.

  6. Go back to the first tab Run and press the Start button to start your search.

Ones the results are written out we suggest to filter the data to a defined confidence with xiFDR.

Notes: