Just came across this project, MZmine is an open-source project delivering a graphical, interactive software for mass-spectrometry data processing.

https://github.com/mzmine

 

An interesting publication for those who use Mass Spectroscopy, PythoMS: A Python Framework to Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data Chemrxiv.

The PythoMS framework introduces a library of classes and a variety of scripts that quickly perform time-consuming tasks: making proprietary output readable; binning intensity vs time data to simulate longer scan times (and hence reduce noise); calculate theoretical isotope patterns and overlay them in histogram form on experimental data (an approach that works even for overlapping signals); render videos that enable zooming into the baseline of intensity vs. time plots (useful to make sense of data collected over a large dynamic range) or that depict the evolution of different species in a time-lapse format; calculate aggregates; and provide a quick first-pass at identifying fragments in MS/MS spectra. PythoMS is a living project that will continue to evolve as additional scripts are developed and deployed.

All available on GitHub under the MIT license https://github.com/larsyunker/PythoMS. This package has been written for python 3.5+.

I've added it to the Spectroscopy page.

 

Just noticed this on Bioconda

r-maldiquant a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

To install

conda install -c bioconda r-maldiquant

More details here http://strimmerlab.org/software/maldiquant/index.html

There are more spectroscopy applications here