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MassMatrix Database Search Engine
NEWS: MassMatrix search engine v2.4.0 has been released to support Ultraviolet Photodissociation (UVPD) and hybrid fragmentations with two or more methods, such as CID/HCD, UVPD/ETD and etc.

MassMatrix Database Search Engine

NEWS: The new PC version of MassMatrix Search Engine has been released in Oct. 2009.
This new free PC version has the cross-link search function.

Go to MassMatrix Search Engine

Introduction

MassMatrix is a newly developed database search software package for tandem mass spectrometric data. It uses a mass accuracy sensitive probabilistic scoring model to rank peptide and protein matches. MassMatrix provides improvements in sensitivity over Mascot and SEQUEST with comparably low false positives. MassMatrix has additional capabilities that set it apart for other algorithms. It is capable of searching through hierarchical MSn (n>=3) spectra (useful in phosphopeptide analysis) where higher confidence in peptide ID can be achieved over MS2 alone. The algorithm is also capable of direct searching of disulfide or chemical cross-linked peptides.


General Features

MS/MS Data: mzXML, MGF, and mzData.

Protein Database: FASTA sequences, MassMatrix BAS format.

Results: Html format.


Unique Aspects

  • Mass Accuracy Sensitive Probabilistic Scoring Model: Pure statistical model that is sensitive to high mass accuracy.
  • Generic Searching Algorithms and Models: Isotope labeling, DNA and RNA sequences and carbohydrate side-chain cleavages.
  • Automated Disulfide Linkage and Chemical Cross-Linkage Searching: Proteins and peptides with disulfide bonds or chemical cross linking can be directly identified without chemical reduction and/or other derivatiization, like normal proteins and peptides.
  • Hierarchical MSn (n>=3) spectral data base searching for peptide: MS2 <=> MSn (n>=3) search algorithm to raise scores and confidence and search peptides with significant neutral loss such as phosphopeptides. This algorithm can be applied to identify peptides that are difficult to be identified only by MS2 spectra, such as peptides with multiple phosphorylation sites.
  • RPLC Retention Time Prediction Model: Retention time is predicted by peptides' hydrophobicity. A statistical score provided based on the model.
  • Handling Low Quality Spectra: Built-in dynamic noise level (DNL) filtering algorithm to filter noise peaks.

Quantitation

1) 4,8-plex iTRAQTM
2) 2,6-plex TMT (Thermo Pierce);


Publications

1) Hua Xu, Michael A. Freitas BMC Bioinformatics 2007, 8, 133 (Link)
2) Hua Xu, Michael A. Freitas J. Proteome Res. 2008, 7(1), 138-144 (Link)
3) Hua Xu, Liwen Zhang, Michael A. Freitas J. Proteome Res. 2008, 7(7), 2605-2615 (Link)
4) Hua Xu, Lanhao Yang, Michael A. Freitas BMC Bioinformatics 2008, 9, 347 (Link)
5) Hua Xu, Michael A. Freitas Proteomics 2009, 9(6), 1548-1555 (Link)
6) Hua Xu, Liwen Wang, Larry Sallans, Michael A. Freitas Proteomics 2009, 9(7), 1763-1770 (Link)
7) Hua Xu, Michael A. Freitas Bioinformatics 2009, 25(10), 1341-1343 (Link)

Go to MassMatrix Search Engine

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Design&Author: Hua Xu