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compareMS2

compareMS2 is a tool for direct comparison of tandem mass spectrometry datasets, typically from liquid chromatography-tandem mass spectrometry (LC-MS/MS), defining a distance as a function of the share of similar spectra. Applications span biomedicine, phylogenetics, forensics and food science.

Forensics
mass spectrometry
phylogenetics
+ 1

JavaScript
C
HTML
+ 2

PIQMIe

A web tool for mass spectrometry-based proteomics data analyses

Data Analysis
mass spectrometry
Optimized data handling
+ 2

HTML
JavaScript
Python
+ 3

mzRecal

mzRecal recalibrates mass spectrometry (MS1) data in mzML format, using peptide identifications in mzIdentML.

mass spectrometry
proteomics

Go
Shell
R
+ 2

OpenMS

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.

C++
mass spectrometry
metabolomics
+ 1

C++
MAXScript
Cython
+ 15

aiproteomics

Generate and compare deep learning models for generating synthetic mass spectral libraries

Machine learning
mass spectrometry
phosphoproteomics
+ 1

Jupyter Notebook
Python
Shell

Mass Spec Studio for Clinical Proteomics

A fusion of the popular OpenMS suite of functionality with the powerful Mass Spec Studio. Users have access to OpenDIA and OpenPRM to support large scale processing of clinical proteomics data sets.

mass spectrometry
proteins
proteomics