Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Downstream analysis (targeted MS-based proteomic analysis)

Downstream analysis programs for targeted MS-based proteomic analysis.

Skyline
Desktop

Skyline

A freely-available and open source Windows client application for building…

A freely-available and open source Windows client application for building selected reaction monitoring (SRM)/multiple reaction monitoring (MRM), parallel reaction monitoring (PRM - targeted MS/MS),…

OpenMS
Desktop

OpenMS

Allows to manage and analyse Liquid chromatography coupled to mass spectrometry…

Allows to manage and analyse Liquid chromatography coupled to mass spectrometry (LC-MS) data. OpenMS is a programming library and tool collection integrated into full-featured workflow systems, such…

GNPS
Dataset

GNPS Global Natural Products Social Molecular Networking

An open-access knowledge base for community-wide organization and sharing of…

An open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS provides a community-led knowledge space in which…

OpenSWATH
Desktop

OpenSWATH

A proteomics software that allows analysis of LC-MS/MS DIA (data independent…

A proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) data. OpenSWATH was designed and optimized to work with profile data. While the software will run on…

mQuest/mProphet
Desktop

mQuest/mProphet

Provides probabilistic scoring of targeted peptide identifications and…

Provides probabilistic scoring of targeted peptide identifications and comprehensive quantification.

TRIC
Desktop

TRIC

An alignment software for targeted proteomics (SRM or SWATH-MS) data. TRIC uses…

An alignment software for targeted proteomics (SRM or SWATH-MS) data. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate information from all…

SWATHProphet
Desktop

SWATHProphet

Analyzes data-independent acquisition (DIA) mass spectrometry (MS) data with…

Analyzes data-independent acquisition (DIA) mass spectrometry (MS) data with precursor ion assays of a spectral library. SWATHProphet can detect fragment ion interferences. They can be removed either…

AuDIT
Desktop

AuDIT

Provides an automated method of objectively evaluating MRM-MS data to identify…

Provides an automated method of objectively evaluating MRM-MS data to identify inaccurate transition data based on the presence of interfering signal or inconsistent recovery between replicate…

TIQAM
Desktop

TIQAM Targeted Identification for Quantitative Analysis by MRM

Developed as a suite of software tools to support targeted identification and…

Developed as a suite of software tools to support targeted identification and quantification using multiple reaction monitoring (MRM) mass spectum technology.

SRMstats
Desktop

SRMstats

A statistical framework is proposed for protein quantification in SRM…

A statistical framework is proposed for protein quantification in SRM experiments based on a family of linear mixed-effects models.

SWATH2stats
Desktop

SWATH2stats

A package intended to transform SWATH data from the OpenSWATH software into a…

A package intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation. SWATH2stats…

ATAQS
Desktop

ATAQS Automated and Targeted Analysis with Quantitative SRM

An integrated software platform that supports all stages of targeted, SRM-based…

An integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post-acquisition data analysis.

QuaSAR
Desktop

QuaSAR

Implements a comprehensive and easy to use pipeline for the analysis of MRM-MS…

Implements a comprehensive and easy to use pipeline for the analysis of MRM-MS data that draws upon both novel and many previously published methods.

MAPDIA
Desktop

MAPDIA

A software package for statistical analysis of differential protein expression…

A software package for statistical analysis of differential protein expression using DIA fragment-level intensities. The workflow consists of three major steps: intensity normalization,…

MSstats
Desktop

MSstats

An R package for statistical relative quantification of proteins and peptides…

An R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows…

LFQuant
Desktop

LFQuant label-free fast quantitative

Analyses high-resolution LC-MS/MS proteomics data based on database searching.…

Analyses high-resolution LC-MS/MS proteomics data based on database searching. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and…

PeakView
Desktop

PeakView

A stand-alone software application that is compatible with all SCIEX mass…

A stand-alone software application that is compatible with all SCIEX mass spectrometer systems for the quantitative review of LC/MS and MS/MS data. PeakView® enables exploration and interpretation…

Spectronaut
Desktop

Spectronaut

Professional software that enables fully automated, fast and accurate signal…

Professional software that enables fully automated, fast and accurate signal processing of SWATH and DIA data sets (HRM-MS). HRM-MS is the next generation targeted proteomics technology invented at…

MassLynx MS…
Desktop

MassLynx MS Software

Allows to acquire, analyze, manage, and share mass spectrometry (MS)…

Allows to acquire, analyze, manage, and share mass spectrometry (MS) information.

Pinpoint
Desktop

Pinpoint

Simplifies the creation of targeted quantitative assays.

Simplifies the creation of targeted quantitative assays.

MultiQuant
Desktop

MultiQuant

A package that enables processing of multiple analytes and samples at the same…

A package that enables processing of multiple analytes and samples at the same time.

MRMer
Desktop

MRMer

Allows to manage highly complex multiple reaction monitoring mass spectrometry…

Allows to manage highly complex multiple reaction monitoring mass spectrometry (MRM-MS) experiments. MRMer functions in an instrument-agnostic fashion using an updated standard of the mzXML format.…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.