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Data conversion and data handling (MS-based proteomic analysis)

Data conversion and data handling programs for MS-based proteomic analysis.

ProteoWizard
Desktop

ProteoWizard

Enables rapid tool creation by providing a robust, pluggable development…

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.

PRIDE Converter
Desktop

PRIDE Converter PRoteomics IDEntification Converter

Allows users to convert search result files into PRIDE XML, generate mzTab…

Allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by…

jmzReader
Desktop

jmzReader

A collection of Java application programming interfaces (APIs) to parse the…

A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML.

jmzIdentML API
Desktop

jmzIdentML API

A Java application programming interface (API) for the Human Proteome…

A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data.

thermo-msf-pars…
Desktop

thermo-msf-parser

A Java library to parse the msf files that constitute the output of Proteome…

A Java library to parse the msf files that constitute the output of Proteome Discoverer.

pymzML
Desktop

pymzML

An extension to Python that offers (i) an easy access to mass spectrometry (MS)…

An extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to…

jmzML
Desktop

jmzML

Allows users to process mzML files using Java programming language. jmzML is a…

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…

RawConverter
Desktop

RawConverter

A mass spectrometry data converter. RawConverter provides the ability to take…

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…

XTandem Parser
Desktop

XTandem Parser

An open-source Java library that parses X!Tandem XML result files into an…

An open-source Java library that parses X!Tandem XML result files into an easily accessible and fully functional object model.

jTraML
Desktop

jTraML

A Java API for the Proteomics Standards Initiative TraML data standard. jTraML…

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…

libmgf
Desktop

libmgf

Allows to parse Mascot Generic Format (MGF). libmgf provides an interface which…

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…

jmzTab
Desktop

jmzTab

Allows to read, write and validate mzTab files. jmzTab is an open source Java…

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.…

mzR
Desktop

mzR

Provides a unified API to the common file formats and parsers available for…

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…

Libfbi
Desktop

Libfbi

A standard C++, header-only template implementation for fast box intersection…

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…

compomics-utili…
Desktop

compomics-utilities

A library containing code shared by many of our research projects, amongst…

A library containing code shared by many of our research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc.

TrackHubGenerat…
Desktop

TrackHubGenerator

Assists in generating track hubs derived from outputs obtained from the PoGo…

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…

Thermo Raw…
Desktop

Thermo Raw File Reader

Provides several methods for parsing the information returned by MSFileReader.…

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…

Concatenated…
Desktop

Concatenated Text File Splitter

Splits apart the concatenated file to re-create the individual text files…

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…

FlexibleFileSor…
Desktop

FlexibleFileSortUtility

Sorts a text file alphabetically (forward or reverse). FlexibleFileSortUtility…

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…

Peptide Hit…
Desktop

Peptide Hit Results Processor

Converts a MSGF+ TSV file, X!Tandem results file (XML format), or a SEQUEST…

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…

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