MassMatrix Search Engine

Public Beta

PUBLIC BETA
Thank you for using the public beta. Please be patient as we correct problems.

MassMatrix PC Beta 1 Ready for Download!

This public beta version of MassMatrix is free for non-commercial use. To obtain a current licensed copy follow the directions below.

Details of the scoring models in MassMatrix can be found in the manuscript:

Hua Xu, Michael A. Freitas BMC Bioinformatics 2007, 8, 133

Details of the disulfide search algorithm in MassMatrix can be found in the manuscript:

Hua Xu, Liwen Zhang, Michael A. Freitas J. Proteome Res. 2008, 7, 138

Quick Start Instructions

  • 1. Download MassMatrix PC
  • 2. Install to the folder C:\Program Files\MassMatrix\
  • 3. Under the program group run "Get License Key" to obtain a unique machine ID.
  • 4. Email the machine ID to license(at)massmatrix.net. In your license request, please include your NAME, TITLE, INSTITUTION/COMPANY, and EMAIL ADDRESS. If you want to install several copies of MassMatrix on several computers, please email the machine IDs for all computers in separate emails.
  • 5. Upon receiving you license file, copy it to C:\Program Files\MassMatrix\.
  • 6. Only three protein databases are included with the installer. You can add databases (FASTA format) to the folder C:\Program Files\MassMatrix\databases.

MassMatrix Noise Filtering Ready for Beta Testing!

This public beta version of MassMatrix DNL is free for non-commercial use. Use this program to filter noise from LC-MS/MS spectra.

Quick Start Instructions

  • 1. Download MassMatrix DNL
  • 2. Unzip the archive
  • 3. Follow the instructions in the README file.

MassMatrix Retention Time Analysis is ready for Beta Testing!

This public beta version of MassMatrix LR_RT is free for non-commercial use. Use this program to score peptide matches from database search programs (MassMatrix, Mascot, X!Tandem and among others) based on their predicted retention time.

Quick Start Instructions

  • 1. Download MassMatrix LR_RT
  • 2. Unzip the archive
  • 3. Follow the instructions in the README file.

Example MS/MS Data for Retention Time Anaylsis

  • 1. Download MassMatrix LR_RT Example data
  • 2. Unzip the archive
  • 3. Follow the instructions in the README file.

Database Search Result Extraction Tools

These tools are used to extract search results from database search programs, MassMatrix, Mascot, OMSSA and X!Tandem, to tab delimited .TXT files

    Download Database search result extraction tools

Data Set with High Mass Accuracy for Evaluating Mass Accuracy-Sensitive Score Algorithms

    Download Data for Mass Accuracy-Sensitive score algorithm evaluation

Data Sets for Evaluating Monte Carlo Simulation Based Score Algorithms

    Download Data for MCS score algorithm evaluation

MassMatrix Input File Tools

These tools convert between common input formats. 1. mzXML2mgf 2. mzXML2mgf_for_MS3 3. ReAdW_patch

Quick Start Instructions

  • 1. Download Input File Tools
  • 2. Unzip the archive
  • 3. Follow the instructions in the README file.

Perl scripts for hierarchical MS2/MS3 database search paper

These tools extract search results from the original result files of MassMatrix, Mascot and X!Tandem and merge the MS2 and MS3 search results to a combined list of peptide matches.

Quick Start Instructions

  • 1. Download Perl scripts for MS2/MS3 database search
  • 2. Unzip the archive
  • 3. Follow the instructions in the README file.

Support

For support questions email support(at)massmatrix.net or post your questions to the google groups support forum.