Spectrum Identification Machine


Spectrum Identification Machine - SIM is a Peptide Spectrum Match - PSM search tool that capitalizes on the high intensity b1 fragment ion of tandem mass spectra of peptides coupled in solution with Phenylisotiocyanate - PITC to confidently sequence the first amino acid and ultimately reduce the search space. This tool enables to make a search with sample without PITC labeling too.

SIM is user-friendly, simple and provides a graphical user interface.

Cross-link Module

State of the art structural mass spectrometry based proteomics is often accomplished by using cross-linkers to covalently bind two or more reactive groups. This strategy is complementary to classical structural biology and therefore broadens the toolset for analyzing protein and protein-protein complex structures. One of the greatest challenges in identifying cross-linked peptides in complex protein mixtures is computationally dealing with the large search space which grows exponentially with each peptide included in the sequence database. Spectrum Identification Machine for Cross-Linked peptides (SIM-XL) is an algorithm to deal with this problem. It capitalizes on experimental features that allow us to effectively address the massive combinatorial problem at hand. SIM-XL is recommended for dealing with the studies of protein-structure and protein-protein-interaction in either simple or complex protein mixtures.

This module is being developed in collaboration with Dalton Mass Spectrometry Lab.

Spectrum Identification Machine can be freely downloaded and installed with a single click of the mouse from the project's Web site.

Supplementary Files

Necessary Resources


A computer capable of running Windows XP with Service Pack 3 or later, Vista, Windows 7 or Windows 8.

A computer with a minimum of 4 GB RAM and 2 or more computing cores is recommended.


Windows XP with Service Pack 3 (or later), Windows Vista, Windows 7 or Windows 8.

For reading RAW Files you must install the Thermo's reader. More information at MSFileReader. The RAW format is a proprietary format of the Thermo Scientific.

The .NET framework 4.5 and Windows Installer 4.5, which can be automatically and freely updated by SIM during installation if necessary.


For performing search, use MS2, MGF or RAW files to create tandem mass spectra. For creating protein database, use FASTA, T-R or MR-PR files.

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For more information, access Computational Proteomics Brazil