Mass spectrometry-based untargeted proteomic software tools

A number of technologies can be used to study proteomes, but arguably none is more powerful than mass spectrometry (MS; Aebersold and Mann, 2003; Cravatt et al., 2007; Domon and Aebersold, 2010). There are two fundamentally different MS-based strategies for analyzing proteomes:…

MS-based untargeted proteomics steps

MS-based untargeted proteomics workflow

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MS-based untargeted proteomics workflow schema

Most recent bioinformatics tools

Informed-Proteo…
Desktop

Informed-Proteomics

Allows top-down data analysis. Informed-Proteomics is composed of a liquid…

Allows top-down data analysis. Informed-Proteomics is composed of a liquid chromatography mass spectrometry (LC-MS) feature-finding algorithm, a database-search algorithm, and an interactive results…

CIDentify
Desktop

CIDentify Collision-Induced Dissociation identify

Helps to identify unknown peptides by mass spectrometry (MS). CIDentify is a…

Helps to identify unknown peptides by mass spectrometry (MS). CIDentify is a homology-based database search algorithm constructed from the source code for a FASTA homology-based database search…

GlyDB
Dataset

GlyDB

Finds reliably glycopeptides from a few thousand collected tandem mass…

Finds reliably glycopeptides from a few thousand collected tandem mass spectrometry (MS/MS) spectra. The GlyDB approach was developed for annotation of low resolution spectra generated by ion trap…

MSBlender
Desktop

MSBlender

Improves identification of peptide-spectrum matches (PSMs) at low error rate.…

Improves identification of peptide-spectrum matches (PSMs) at low error rate. MSBlender is a unified probabilistic approach that delivers a method to estimate correct integrated error rates even…

Most popular analytical software

Xlink Analyzer
Desktop

Xlink Analyzer

A software tool for visualization and analysis of cross-linking mass…

A software tool for visualization and analysis of cross-linking mass spectrometry (XL-MS) data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of…

Metriculator
Desktop

Metriculator

A software tool designed to facilitate long-term storage of extensive…

A software tool designed to facilitate long-term storage of extensive performance metrics. Metriculator features a web interface that generates interactive comparison plots for contextual…

BatMass
Desktop

BatMass

A software package which allows to perform quick quality control of raw LC/MS…

A software package which allows to perform quick quality control of raw LC/MS data through its fast visualization capabilities. BatMass also serves as a testbed for developers of LC/MS data…

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…

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