Converts mass spectrometry (MS) proteomics data sets into PRIDE XML for submission to online database PRIDE. PRIDE Converter allows users to create mzTab skeleton files that can be used to submit quantitative and gel-based MS data. It can filter out contaminants and empty spectra by combining multiple PRIDE XML files together. A graphical and a command line interfaces are available and support the integration of novel pipelines.
Manages proteomic mass spectrometry workflows and data analysis. Multiplierz provides a toolset of multiple methods for peptide identification, quantitation, reporting, as well as tools for easily manipulating standard data formats. This software is a Python library compatible with new reporting formats and high-level tools to achieve post-perform proteomic analyses. The architecture of the software environment has seamless integration with native data files via mzAPI.
Investigates mass spectrometry datasets. pymzML can serve to develop tailored pipelines for non-standard data analysis. It permits users to display customizable annotated mass spectra and ion chromatograms. This tool consists of an extension to Python that offers (i) an access to mass spectrometry (MS) data, allowing the development of tools, (ii) a parser for mzML data and (iii) a set of functions to compare or handle spectra.
A mass spectrometry data converter. RawConverter provides the ability to take advantage of the high resolution and accuracy provided by the latest Thermo Fisher instruments. RawConverter extracts mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data from RAW files like its predecessor RawXtract but also selects the correct precursor mass-to-charge (m/z) ratios. It accepts RAW data generated by either data-dependent acquisition (DDA) or data-independent acquisition (DIA). The output file format can be MS1/MS2, MGF or mzXML.
A standard C++, header-only template implementation for fast box intersection in an arbitrary number of dimensions, with arbitrary data types in each dimension. The implementation is applied to a data aggregation task on state-of-the-art liquid chromatography/mass spectrometry data, where it shows excellent run time properties.
Calibrates mass spectrometry (MS) data files. MZRefinery can evaluate up to three different calibration methods by using confident peptide spectrum matches and removes systematic bias via an optimal transform function. The software is implemented within the msConvert program which is part of the ProteoWizard suite. This affiliation allows a native compatibility with a large variety of file formats for the inputs and outputs.
Provides an interface for basic analysis of mass spectrometry data. mzDesktop gives access to the proteomic analysis algorithms from the library of the Multiplierz software. This software offers several functions existing in Multiplierz but through a graphical user interface. Users can visualize the degree of protein sequence coverage supported by given set of peptide-spectrum match (PSM). It is compatible with mzReports and mzIdentML files.
A Java API for the Proteomics Standards Initiative TraML data standard. jTraML provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions.
Allows to parse Mascot Generic Format (MGF). libmgf provides an interface which can easily be integrated into existing C++ projects, adapted to managed code environments or bridged to scripting languages such as Python or R.
Allows users to process mzML files using Java programming language. jmzML is a mature Java application programming interface (API) for mzML files that combines a small memory footprint with a fully functional object model, including automatic XML reference resolving without sacrificing the overall speed of data access. This software comes with an interactive mzML viewer that can be used to load and view spectra and chromatograms from multiple, very large mzML files simultaneously.
Allows to read, write and validate mzTab files. jmzTab is an open source Java application programming interface for to supporting the Proteomics Standards Initiative (PSI)’s mzTab standard format. The software simplifies accessing the information included in mzTab files, thereby promoting its use and facilitating its support in third party software. jmzTab is structured in a three-layer architecture: (i) the Core Model Layer, (ii) the Enhancement Utilities Layer and (iii) the Standalone Application Layer.
Allows conversion of convert tandem mass spectrometry (MS/MS) data obtained using Applied Biosystem's QStar and QTrap 2000 and 4000 series. wiff2dta has two modes of user interaction: (1) a graphical user interface (GUI) that requires user interaction (GUI-mode), and (2) command-line parameters with no user interaction required (batch-mode). The software can be started in multiple instances, resulting in parallel processing. wiff2dta can be integrated in automation and high throughput environments.
Provides a tool for mass spectrometry data visualization, annotation, and notebooking. mzStudio allows researchers to corroborate peptide-spectral-matches and associated quantitative measures across large, multidimensional liquid chromatography tandem-mass spectrometry (LC-MS/MS) data sets. Instrument platforms and search engines are also concerned. This software is appropriate to assist for describing novel modifications or surprising gas phase fragmentation behavior.
Converts a MSGF+ TSV file, X!Tandem results file (XML format), or a SEQUEST Synopsis/First Hits file to a series of tab-delimited text files summarizing the results. Peptide Hit Results Processor permits creation of parallel files that contains sequence information, modification details, and protein information. The user can optionally provide a modification definition file that specifies the symbol to use for each modification mass.
Provides a unified API to the common file formats and parsers available for mass spectrometry data. mzR comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
Splits apart the concatenated file to re-create the individual text files (creating one file per spectrum). Concatenated Text File Splitter is a package that permits to re-search the data with SEQUEST (which reads individual .Dta files).
Sorts a text file alphabetically (forward or reverse). FlexibleFileSortUtility supports both in-memory sorts for smaller files and use of temporary swap files for large files. It can alternatively sort on a column in a tab-delimited or comma-separated file. The column sort mode also supports numeric sorting.
Recalibrates PKL files derived from mass spectrometry (MS)-experiments. AdjustPKL enables users to shift all m/z values of this kind of file. It permits to choose to shift all spectra or just a single one of the file. This tool provides a small spectrum viewer to visually validate the resulting spectra.
Provides several methods for parsing the information returned by MSFileReader. Thermo Raw File Reader is a package that demonstrates how to read Thermo-Finnigan .Raw files using Thermo's MS File Reader. It offers some functions to determine the parent ion m/z and fragmentation mode in a given scan filter, to determine the ionization mode from a given scan filter, to extract multiple reaction monitoring (MRM) masses listed in a given scan filter and many others.
Assists in generating track hubs derived from outputs obtained from the PoGo software. TrackHubGenerator allows users to create an appropriated folder for being exploitable with genome browsers such as UCSC Genome Browser or BioDalliance.
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.