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Data simulation software tools| MS-based untargeted proteomics

The most important step in any quantitative proteomic pipeline is feature detection (aka peak picking). However, generating quality hand-annotated data sets to validate the algorithms, especially for lower abundance peaks, is nearly impossible. An…
GDG
Desktop

GDG Glycopeptide Decoy Generator

Enables determination of the accuracy of tools that assign glycopeptides to…

Enables determination of the accuracy of tools that assign glycopeptides to collision-induced dissociation (CID) data. GDG is a graphical method to generate glycopeptide decoys de novo. The software…

MSAcquisitionSi…
Desktop

MSAcquisitionSimulator

A collection of C++ programs for simulating ground truth LC-MS data and the…

A collection of C++ programs for simulating ground truth LC-MS data and the subsequent application of custom data-dependent acquisition (DDA) algorithms. MSAcquisitionSimulator consists of three…

JAMSS
Desktop

JAMSS Java Mass Spectrometry Simulator

A fast, self-contained in silico simulator capable of generating simulated MS…

A fast, self-contained in silico simulator capable of generating simulated MS and LC-MS runs while providing meta information on the provenance of each generated signal. JAMSS improves upon previous…

Mspire-Simulato…
Desktop

Mspire-Simulator

A free, open-source shotgun proteomic simulator that goes beyond previous…

A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components.…

OpenMS-Simulato…
Desktop

OpenMS-Simulator

An open-source software package to predict theoretical spectrum for a given…

An open-source software package to predict theoretical spectrum for a given peptide sequence. Based on the mobile-proton hypothesis for peptide fragmentation, OpenMS-Simulator trained a closed-form…

SSRCalc
Web

SSRCalc Sequence Specific Retention Calculator

Calculates sequence-specific retention for the accurate peptide retention…

Calculates sequence-specific retention for the accurate peptide retention prediction in RP HPLC (Reverse Phase High-Performance Liquid Chromatography). SSRCalc was developed in conjunction with…

MSSimulator
Desktop

MSSimulator

A simulation software for LC-MS and LC-MS/MS experiments. Starting from a list…

A simulation software for LC-MS and LC-MS/MS experiments. Starting from a list of proteins from a FASTA file, the simulation will perform in-silico digestion, retention time prediction, ionization…

2DE Tandem MS
Desktop

2DE Tandem MS

A computer program designed for use in the biochemistry, proteomics, or…

A computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations—2D electrophoresis and tandem mass spectrometry both designed for use…

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