MassMatrix Downloads
1. MassMatrix Suite for Windows XP (32/64 bit) and Windows 7 (32/64 bit)
:
The new version of MassMatrix for Windows PC (XP/7, 32/64bit) is now available. This PC version is a software suite for protein identification/characterization, cross-link/disulfide search, iTRAQ/TMT quantitation, and
15N/SILAC quantitation using LC-MS/MS.
The new MassMatrix Suite for Windows PC is freely availabe. To obtain a current version, please follow the directions below.
1. Download MassMatrix Suite for PC using the above link.
2. Follow the installation wizard to install MassMatrix on your comptuer.
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, intall it on your computer.
6. IPI protein databases are included in the distribution. You may download and install the complete sets of NCBInr and Uni-Prot databases via the above link.
Note: An administrator account is required to install and run MassMatrix on Windows.
2. MM Result Extract:
The tool is used to extract MassMatrix search results to a spreadsheet.
3. MM File Conversion Tools:
These tools convert between common input formats: .RAW (Thermo), .mzXML, .MGF.
Video tutorial at YouTube: click here
Important notes for Mascot users:
Due to the fact that Mascot doesn't search spectra with charges >= +8, it will sometimes warn you that invalid charges are found in your MGF files during searching. Please ignore the warning and it will not negativelly affect your results. Those spectra with charges >= +8, however, are real spectra with high charges and can be positively identified in other search programs, such as MassMatrix.
4. MM Automated LC-MS/MS System Diagnostic Tool:
MassMatrix LC-MS/MS system diagnosis provides fully automated and real-time system diagnosis. The program is built based on MassMatrix database search program (www.massmatrix.net). The current release is targeted to system diagnosis of LCQ, LTQ, LTQ-Orbitrap and LTQ-FTICR mass spectrometers (ThermoFinigan, CA, USA).
5. Tools for Generating Decoy Protein Databases:
These tools are used to generate decoy protein databases (reversed or randomized protein sequences from the original protein databases).
6. MassMatrix Retention Time Analysis:
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.
7. MassMatrix Noise Filtering:
This public beta version of MassMatrix DNL is free for non-commercial use. Use this program to filter noise from LC-MS/MS spectra.
8. Quantitation Analysis for N15 Labeling:
The software is under beta testing, for more information, please contact Hua Xu at hxx58@case.edu.
9. Multiple-Way Comparison:
The software is under beta testing, for more information, please contact Hua Xu at hxx58@case.edu.
10. XMapper:
XMapper is a software tool used to map and score the cross-links in proteins and peptides by use of MassMatrix database search results. The results are displayed in color maps, called X-Maps, and also in .CSV files for further analysis.
Video tutorial at YouTube (< 10 min): click here
For more information, please contact Hua Xu at hxx58@case.edu.
