Data conversion and data handling programs for MS-based proteomic analysis.
Enables rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations.
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.
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.
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.
A graphical user interface (GUI) for rapid composition of HPLC–MS analysis workflows.
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.