SIM-XL - Spectrum Identification Machine for Cross-linked Peptides



Spectrum Identification Machine for Cross-linked Peptides (SIM-XL) can be freely downloaded and installed with a single click on the Download button.

Publication Details

Supplementary Files

  • SIM-XL output files (*.simxlr) and parameter file can be downloaded here.
  • RAW and mzIdentML output files can be downloaded at PRIDE Repository.
  • We use a FASTA database containing the sequence of Hsp90 plus five decoys for performing the search.



⇒ A computer with at least a 4 GB RAM and 2 computing cores is recommended.


⇒ Windows 7 (32 or 64 bits) or later.

⇒ For reading Thermo RAW files, the MSFileReader must be installed by creating an account at Thermo®, then logging and choosing Utility Software.

⇒ The .NET framework 4.5, which will be automatically updated by SIM-XL if necessary.

⇒ For opening the structural script to visualize the 3D model protein, the PyMOL must be installed.

Data files

⇒ SIM-XL v1.2 is compatible with data files in the formats mzML 1.1.0, MS2, Mascot Generic Format (MGF), Waters® RAW files and can work directly with Thermo RAW files if the freely available MSFileReader is locally installed.

⇒ SIM-XL exports results to its own format (i.e., *.simxlr) and in the mzIdentlML 1.2 draft, format that is currently under development by the HUPO Proteomics Standards Initiative to support the identification of cross-linked peptides. We note this is the first search engine that enables complete submissions of XL-MS data to PRIDE, being therefore is compatible with the PRIDE Inspector software.

SIM-XL uses Comet® to perform pre-search in Dynamic DB Reduction Mode.