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

Mass spectrometry-based untargeted proteomic software tools

Most Recent Tools

Progenesis QI
Desktop

Progenesis QI

Allows to analyze small molecule concerning liquid chromatography-mass…

Allows to analyze small molecule concerning liquid chromatography-mass spectrometry (LC-MS) data. Progenesis QI includes a search engine named Metascope. The characteristics of this tool (peak…

Decision Forest
Desktop

Decision Forest

Outperforms decision tree in both training and validation. Decision forest is…

Outperforms decision tree in both training and validation. Decision forest is an ensemble method developed by combining the predictions from multiple independent decision tree models to reach a…

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…

xTract
Desktop

xTract

Encompasses a suite of algorithms that allows the automated processing and…

Encompasses a suite of algorithms that allows the automated processing and statistical validation of quantitative data from quantitative chemical cross-linking-mass spectrometry (qCX-MS) experiments.…

Most Popular Tools

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

An algorithm to align LC-MS samples and to match corresponding ion species…

An algorithm to align LC-MS samples and to match corresponding ion species across samples.

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