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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

Mascot…
Desktop

Mascot Percolator

Interfaces Mascot with Percolator. Mascot Percolator is an extension that works…

Interfaces Mascot with Percolator. Mascot Percolator is an extension that works in 3 steps: (i) reads the Mascot results files, (ii) computes the scoring features and uses these for the Percolator…

DecoyPYrat
Desktop

DecoyPYrat

Allows quick generation of decoy databases for both separate and concatenated…

Allows quick generation of decoy databases for both separate and concatenated searches. DecoyPyrat is an efficient open source application that significantly reduces the inaccuracy in decoy…

Seven Golden…
Desktop

Seven Golden Rules

Automatically excludes wrong molecular formulas. Seven Golden Rules consists in…

Automatically excludes wrong molecular formulas. Seven Golden Rules consists in (1) applying heuristic restrictions for number of elements during formula generation, (2) performing LEWIS and SENIOR…

SPLASH
Desktop

SPLASH SPectraL hASH

Finds all the spectra that correspond to a specific compound across different…

Finds all the spectra that correspond to a specific compound across different databases. SPLASH is a database-independent spectrum identifier that contains separate blocks for defining different…

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…

MALDIViz
Web

MALDIViz

Facilitates visualization, statistical analysis, and high-quality image and…

Facilitates visualization, statistical analysis, and high-quality image and data export. MALDIViz is a comprehensive informatics application for MALDI HTS data. This package provides a theme on top…

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