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Interpretation prediction (untargeted MS-based proteomic analysis)

Interpretation prediction programs for untargeted MS-based proteomic analysis.

PeptideShaker
Desktop

PeptideShaker

A search engine independent platform for interpretation of proteomics…

A search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet,…

Group-DIA
Desktop

Group-DIA

Analyzes multiple data-independent acquisition (DIA) data files simultaneously.…

Analyzes multiple data-independent acquisition (DIA) data files simultaneously. Group-DIA is an untargeted analysis method which combines the elution profiles of precursor ions and fragment ions from…

Peptigram
Web

Peptigram

Is dedicated to the visualization and comparison of peptides detected by Tandem…

Is dedicated to the visualization and comparison of peptides detected by Tandem mass spectrometry (MS/MS). The principal advantage of Peptigram is that it provides visualizations at both the protein…

MS-GF
Desktop

MS-GF MS GeneratingFunction

Determines the validity of peptide identification by calculating p-values from…

Determines the validity of peptide identification by calculating p-values from tandem mass spectra (MS/MS). MS-GF can be used in addition to the decoy searches or on its own. The software can also…

proBAMtools
Desktop

proBAMtools

Performs various analyses based on the proBAM files. proBAMtools includes…

Performs various analyses based on the proBAM files. proBAMtools includes functions for genome-based proteomics data interpretation, protein and gene inference, count-based quantification, and data…

RAMM
Desktop

RAMM RNAModMapper

Allows interpretation of collisional-induced dissociation (CID) data from…

Allows interpretation of collisional-induced dissociation (CID) data from oligonucleotides. RAMM can map interpreted tandem mass spectrometry (MS/MS) sequences onto RNA sequences. It enables higher…

Pride-asap
Desktop

Pride-asap

An open source software application and library written in Java that provides a…

An open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database.

SPA
Desktop

SPA Sparse Proteomics Analysis

Finds optimal feature vectors which are extremely sparse, allowing a highly…

Finds optimal feature vectors which are extremely sparse, allowing a highly accurate classification, and robust against noise. Sparse Proteomics Analysis (SPA) is an algorithm based on the theory of…

G T A T C G C T A
SBEAMS
Desktop
PIQMIe
Web
GiaPronto
Web

GiaPronto

Processes data and plots a variety of common and less common graphs for the…

Processes data and plots a variety of common and less common graphs for the analysis of proteomics datasets. GiaPronto is fully automated and provides both quality control and biological…

QARIP
Web
DrDMASS+
Desktop

DrDMASS+

Allows analysis of mass spectral data based on multivariate analysis. DrDMASS+…

Allows analysis of mass spectral data based on multivariate analysis. DrDMASS+ performs four stages: (1) Peak Correction that allows correction of experimental m/z values, (2) Multivariate Data…

PACom
Desktop

PACom Protein Assay Comparator

Permits users to import, integrate, manage and compare numerous proteomics…

Permits users to import, integrate, manage and compare numerous proteomics datasets at the same time. PACOM is a Java standalone tool that provides an innovative, easy-to-use and powerful way of data…

NetWeAvers
Desktop

NetWeAvers Network Weighted Averages

An R package for analyzing groups of regulated proteins in a network context,…

An R package for analyzing groups of regulated proteins in a network context, e.g. as defined by clusters of protein-protein interactions. NetWeAvers provides a method for analyzing proteomics data…

OpenChrom
Desktop

OpenChrom

Provides extension points to enable built-in import capabilities for binary or…

Provides extension points to enable built-in import capabilities for binary or textual instrument vendors’ data formats. OpenChrom is an extensible cross-platform open source software for the mass…

THRASH
Algorithm

THRASH Thorough high resolution analysis of spectra by Horn

A fully automated computer algorithm that can be applied to complex mass…

A fully automated computer algorithm that can be applied to complex mass spectra of peptides and proteins. THRASH uses a subtractive peak finding routine to locate possible isotopic clusters in the…

STRAP PTM
Desktop
Molecular…
Desktop

Molecular networks

It allows spectra to be grouped together in chemical classes, giving…

It allows spectra to be grouped together in chemical classes, giving researchers a much more guided approach to identify novel molecular.

Annotator
Desktop

Annotator

Offers a standardized method of protein selection. Annotator addresses the…

Offers a standardized method of protein selection. Annotator addresses the issue of small sample sizes inherent in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) data by using…

Brukin2D
Desktop

Brukin2D

Provides a way to overview a complete chromatograph analysis. Brukin2D allows…

Provides a way to overview a complete chromatograph analysis. Brukin2D allows visualization, evaluation, procession and comparison of Liquid Chromatography-Mass Spectrometry (LC-MS) data. It…

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