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

Peptide and transition selection (targeted MS-based proteomic analysis)

The design of transitions is critical for the success of MRM experiments, but predicting signal intensity of peptides and fragmentation patterns ab initio is challenging given existing methods.

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),…

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…

DIA-Umpire
Desktop

DIA-Umpire

An open source Java program for computational analysis of data independent…

An open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. DIA-Umpire enables untargeted peptide and protein identification…

SRM Collider
Web
Desktop

SRM Collider Selected Reaction Monitoring Collider

Calculates nonredundant theoretical selected reaction monitoring (SRM) assays.…

Calculates nonredundant theoretical selected reaction monitoring (SRM) assays. SRM Collider is based on predicted retention times and empirical fragment ion intensities to proceed simulations. It can…

MaRiMba
Desktop

MaRiMba

Creates multiple reaction monitoring (MRM) list from any spectral library.…

Creates multiple reaction monitoring (MRM) list from any spectral library. MaRiMba provides users with the ability to fully customize MRM lists to meet their experimental needs. It offers the…

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.

Picky
Web

Picky

Allows to design scheduled parallel reaction monitoring/selected reaction…

Allows to design scheduled parallel reaction monitoring/selected reaction monitoring (PRM/SRM) assays. Picky is a web application that automatically generates optimized and scheduled SRM/PRM assays…

Ariadne
Desktop

Ariadne

Offers reliable and automated analysis of large-scale SRM differential…

Offers reliable and automated analysis of large-scale SRM differential expression studies. To quantify monitored targets, Ariadne exploits metadata imported from the transition lists, and targets can…

PeptidePicker
Web

PeptidePicker

Generates a list of the most appropriate surrogate peptides for target proteins…

Generates a list of the most appropriate surrogate peptides for target proteins to be analyzed by Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry (LC/MRM-MS). PeptidePicker…

MRMPilot…
Desktop

MRMPilot Software

A program that streamlines the building and optimization of peptide MRM…

A program that streamlines the building and optimization of peptide MRM quantitative assays on QTRAP systems and TripleTOF 5600 systems.

MRMaid
Web

MRMaid

Helps you design SRM assays by suggesting peptides and product ions to monitor…

Helps you design SRM assays by suggesting peptides and product ions to monitor based on millions of experimental spectra from the PRIDE database.

Expressionist for MS
Desktop

Expressionist for MS Genedata Expressionist for Mass Spectrometry

Allows you to chain individual data processing steps together to create…

Allows you to chain individual data processing steps together to create specific workflows. It is a single software solution for all instrument vendors that offers full scalability and high analysis…

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.

Information

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