Stand-alone Software

WinProphet
iTop-Q

WinProphet, a lightweight and installation-free Windows-based pro-teomics pipeline software tool. Users can incorporate not only all the functions in TPP but other external programs into their pipelines. WinProphet provides graphical user interfaces which allow users to create, automatically execute, monitor, and reuse the pipeline for proteomics data analysis.

iTop-Q
iTop-Q

We present the first fully automated tool, iTop-Q (intelligent Top-down proteomics Quantitation), for top-down proteomics quantitation using XIC abundances. Instead of utilizing single spectrum for proteoform quantitation, iTop-Q constructs extracted ion chromatograms (XICs) of possible proteoform peaks across adjacent MS1 spectra to calculate abundances for accurate quantitation. Notably, iTop-Q is implemented with a newly proposed algorithm, called DYAMOND, using dynamic programming for charge state deconvolution, instead of using THRASH as in other tools. Furthermore, iTop-Q performs proteoform alignment to support quantitation analysis across replicates/samples. The performance evaluation on an in-house standard data set and a public large-scale yeast lysate data set shows that iTop-Q achieves highly accurate quantitation, more consistent quantitation than using intra-spectrum quantitation. Furthermore, the DYAMOND algorithm is suitable for high charge state deconvolution and can distinguish shared peaks in co-eluting proteoforms.

iMet-Q
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.

MAGIC
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.

IDEAL-Q
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

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

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.

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.