Stand-alone Software

IDEAL-Q  
IDEAL-Q is an automated analysis tool for label-free quantitative proteomics. It accepts mzXML raw data format and Mascot xml and ProtXML/PepXML for identification result. IDEAL-Q uses an elution time prediction and peak alignment algorithms to quantify peptides across different LC-MS runs and increase quantitation coverage. Furthermore, the tool adopts an stringent validation step on Signal-to-noise ratio, Charge state, Isotopic distribution (SCI validation) to ensure quantitation accuracy. IDEAL-Q provides variously optional normalization tools for flexible workflow design such as addition of fractionation strategies and multiple spiked internal standards.
   
Multi-Q  
Multi-Q Web Server provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling method. Multi-Q is designed as a generic platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. In comparison with its previous stand-alone version, this new web server version provides many enhanced features and flexible options for quantitation. The work flow of the web server is represented by a quantitation wizard so that the tool can be easy to use. Furthermore, it provides friendly user interface in output. The web server output a default report for quantitation results. In addition, it allows users to customize their output report and information of user's interest can be easily highlighted. The output provides visualization of mass spectral data so that users can conveniently validate the results.
   
MaXIC-Q  
MaXIC-Q is an automated quantitation tool, which utilizes XICs acquired from isotope labeling techniques for quantitation analysis. As a generic computation platform for high-throughput quantitative proteomics, MaXIC-Q offers the following features: (1) It accepts the mzXML (24) spectral format, which can be converted from raw files of various mass spectrometers by existing tools, as well as search results from commonly used search engines, including Mascot and SEQUEST. (2) It allows user-defined isotope codes, which cover a very broad range of quantitation strategies for various in vivo and in vitro labeling techniques, and even user-developed labeling methods. To the best of our knowledge, MaXIC-Q is currently the only tool that defines stringent criteria for the validation of both XIC and mass spectra to achieve high accuracy in an unattended manner. Furthermore, MaXIC-Q provides graphic interfaces, Elution3D, an XIC viewer, and an ion mass spectrum viewer that allow flexible user-activated interactive modification based on simultaneous 3D visualization of the m/z, elution time and intensity.
   
MAGIC  
MAGIC (Mass spectrometry-based Automated Glycopeptide IdentifiCation platform) is an automated tool for glycopeptide identification and glycan composition determination. MAGIC adopts a novel Trident algorithm for accurate Y1-ion detection and generates in silico peptide MS/MS spectra for database searches. MAGIC provides the flexibility in setting detection criteria, visualization of each spectrum with peak annotated and a summary report for export. MS/MS spectra in Mascot Distiller MGF and Mascot XML are recommended format for input and identification results, respectively.
   
iMet-Q  
iMet-Q (intelligent Metabolomic Quantitation) is an automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. It has a complete quantitation procedure for noise removal, peak detection and peak alignment. In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv and txt format.
   

Other Tools

FileChecker  
FileChecker is an automated tool for validating mzXML and mzML files. Unsuccessful conversion of the raw data will cause problems while being processed by tools requiring mzXML or mzML files as input.
Available functions:
1.Check the existence of the last tag </mzXML> and </mzML> at the end of the mzXML and mzML files, respectively.