Software

mMass

The primary software used for ZooMS analysis is the free and open source software mMass. Although the software can still be downloaded, it is unfortunately no longer being developed or supported. Recently, efforts have been made to keep mMass available and compatible with new computer operating systems (through the European Research Council FINDER project and the Warinner Lab), but additional community support is needed.

• Available at: http://www.mmass.org
• Updates available at: https://github.com/dreamingspires/mMass
• Citation: Niedermeyer THJ, Strohalm M. 2012. mMass as a software tool for the annotation of cyclic peptide tandem mass spectra. PLoS ONE 7(9): e44913.
• Citation: Strohalm M, Kavan D, Novák P, Volný M, Havlíček V (2010) mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. Anal Chem 82(11):4648-4651.
• Citation: Strohalm M, Hassman M, Košata B, Kodíček M (2008) mMass Data Miner: an Open Source Alternative for Mass Spectrometric Data Analysis. Rapid Commun Mass Spec 22(6): 905-908.

Bacollite

The bacollite package offers a set of tools for aligning MALDI spectrum data with ‘theroretical’ peak positions that have been calculated from sequence and chemistry data. The alignment is carried out by cross-corelation and yields a correlation score and a lag score, both of which can be used to determine the presence or absence of a peptide in the spectrum.

• Available at: https://github.com/bioarch-sjh/bacollite
• Citation: S. Hickinbotham, S. Fiddyment, T. L. Stinson, M. J. Collins, How to get your goat: Automated identification of species from MALDI-ToF spectra. Bioinformatics 36, 3719–3725 (2020).