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All-in-one software tools | MS-based untargeted proteomics

TOPPAS
Desktop

TOPPAS The OpenMS Proteomics Pipeline Assistant

A graphical user interface (GUI) for rapid composition of HPLC–MS analysis…

A graphical user interface (GUI) for rapid composition of HPLC–MS analysis workflows.

ProteomeTools
Dataset

ProteomeTools

Translates the human proteome into molecular and digital tools for drug…

Translates the human proteome into molecular and digital tools for drug discovery, personalized medicine and life science research. The ProteomeTools project is a joint effort of the Technical…

PEAKS
Desktop

PEAKS

Identifies peptides from a sequence database with tandem mass spectrometry…

Identifies peptides from a sequence database with tandem mass spectrometry data. PEAKS employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve both the speed…

TPP
Desktop

TPP Trans-Proteomic Pipeline

A collection of integrated tools for MS/MS proteomics, developed at the SPC.

A collection of integrated tools for MS/MS proteomics, developed at the SPC.

TOPP
Desktop

TOPP

Provides a set of computational tools which can be easily combined into…

Provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.

hEIDI
Desktop

hEIDI (h) Exploitation et Integration des Donnees d'Identification

Manages and combines both identifications and semiquantitative data related to…

Manages and combines both identifications and semiquantitative data related to multiple liquid chromatography-mass spectrometry (LC−MS)/MS analyses. hEIDI can be used to compile analyses and…

CPFP
Desktop

CPFP Central Proteomics Facilities Pipeline

Allows to analyse shotgun proteomics data. CPFP is a data analysis pipeline…

Allows to analyse shotgun proteomics data. CPFP is a data analysis pipeline that aims to provide a simple interface for core facility staff and clients, and to fully automate the analysis of tandem…

SpecOMS
Desktop

SpecOMS Spectra Open Modification Search

Handles the computational complexity of pairwise comparisons of spectra in the…

Handles the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics…

MetPP
Desktop

MetPP METabolomics Profiling Pipeline

Analyzes metabolomics data generated from the 2D gas chromatography…

Analyzes metabolomics data generated from the 2D gas chromatography time-of-flight mass spectrometry (GCxGC-TOF MS) instrument. MetPP is able to recognize the concentration difference of the…

DISMS2
Desktop

DISMS2

Calculates proteome-wide distances directly from MS/MS data. DISMS2 allows for…

Calculates proteome-wide distances directly from MS/MS data. DISMS2 allows for the choice of the spectrum distance measure and includes different spectra preprocessing and filtering steps that can be…

QuiXoT
Desktop

QuiXoT

Quantifies thorough statistics and inspects graphical data for any kind of…

Quantifies thorough statistics and inspects graphical data for any kind of high-throughput stable isotope labelling (SIL) experiment on routine basis. QuiXoT allows practically quantification of any…

ProteoCloud
Desktop

ProteoCloud

A Java-based proteomics cloud computing pipeline system for peptide and protein…

A Java-based proteomics cloud computing pipeline system for peptide and protein identifications. The ProteoCloud pipeline consists of three types of units: (i) a single client-side controller unit,…

ICR-2LS
Desktop

ICR-2LS

Finds peaks in raw mass spectra. ICR-2LS is a PC-based software package that…

Finds peaks in raw mass spectra. ICR-2LS is a PC-based software package that supports advanced experimental techniques and automated data analysis. Capabilities include full waveform generation,…

Proteome…
Desktop

Proteome Discoverer

A package for protein identification and quantification in biologic complex…

A package for protein identification and quantification in biologic complex samples. It covers a wide range of possible proteomic analyses from proteins and peptides identification to…

swissPIT
Desktop

swissPIT swiss Protein Identification Toolbox

A project at the Swiss Institute for Bioinformatics (SIB) in Geneva which aims…

A project at the Swiss Institute for Bioinformatics (SIB) in Geneva which aims at the development of an automated analysis system to identify proteins using MS and MS/MS based data.

PhosFox
Desktop

PhosFox

Enables peptide-level processing of phosphoproteomic data generated by multiple…

Enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms, including Mascot, Sequest, and Paragon, as well as cross-comparison of their…

EasyProt
Desktop

EasyProt

A platform for mass spectrometry data processing, protein identification,…

A platform for mass spectrometry data processing, protein identification, quantification and unexpected post-translational modification characterization. EasyProt provides a fully integrated…

MultiAlign
Desktop

MultiAlign

Aligns multiple liquid chromatography-mass spectrometry (LC-MS) datasets to one…

Aligns multiple liquid chromatography-mass spectrometry (LC-MS) datasets to one another by clustering mass and chromatographic elution features across datasets. The MultiAlign application provides…

pkDACLASS
Desktop

pkDACLASS

Provides a complete data analysis solution for the users of MALDI-TOF MS…

Provides a complete data analysis solution for the users of MALDI-TOF MS proteomics raw data especially biomedical researchers with no statistics background. pkDACLASS classifies the samples based on…

MSDK
Desktop

MSDK Mass Spectrometry Development Kit

A Java library of algorithms for processing mass spectrometry data. The goals…

A Java library of algorithms for processing mass spectrometry data. The goals of MSDK are to provide a flexible data model with Java interfaces for mass-spectrometry related objects (including raw…

MassHunter…
Desktop

MassHunter Workstation Software

Provides intuitive, yet powerful, instrument control, data acquisition,…

Provides intuitive, yet powerful, instrument control, data acquisition, qualitative and quantitative data analysis, and reporting for Agilent time-of-flight (TOF), quadrupole time-of-flight (Q-TOF),…

Visualize
Desktop

Visualize

Provides a comprehensive proteomics data analysis method. Visualize is a…

Provides a comprehensive proteomics data analysis method. Visualize is a workstation application with an intuitive graphical user interface (GUI). It brings together different approaches to examine…

Firmiana
Web

Firmiana

Allows scientists to deposit mass spectrometry (MS) raw files, perform proteome…

Allows scientists to deposit mass spectrometry (MS) raw files, perform proteome identification and quantification online, carry out bioinformatics analyses, and extract knowledge. Firmiana offers a…

MALDIViz
Web

MALDIViz

Can be used to do quality checks, visualizations and analysis of mass…

Can be used to do quality checks, visualizations and analysis of mass spectrometry data. MALDIViz App is a Shiny-based Web application, accessible independently of the operating system and without…

STEM
Desktop

STEM STrategic Extractor for Mascot's results

Processes large-scale mass spectrometry-based proteomics data. STEM is a…

Processes large-scale mass spectrometry-based proteomics data. STEM is a stand-alone computational tool that evaluates, integrates, and compares large datasets produced by Mascot. STEM is compatible…

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