SoftwareApplication
identifier: 10.5281/zenodo.14990300
name: compareMS2
description: compareMS2 is a tool for direct comparison of tandem mass spectrometry (MS/MS) datasets, typically from LC-MS/MS, in proteomics or metabolomics, defining a distance as a function of the share of similar spectra. Applications span biomedicine, phylogenetics, forensics, ecology and food science.
description: compareMS2 calculates the similarity between tandem mass spectrometry datasets and visualizes the results in a phylogenetic tree. * Only mass spectrometry data is needed * Relative distances between samples immediately become clear * A Graphical User Interface simplifies usage * Optionally, sample files can be mapped to species names * Phylogenetic trees can be saved in several graphics file formats for direct use in publications * Input consists of MS2 data in MGF format * Output file formats are compatible with common phylogenetic tree software (for instance [MEGA](https://www.megasoftware.net/)) for further analysis and visualization
code repository: https://github.com/524D/compareMS2
code repository: https://github.com/524D/compareMS2-cmd
author: https://orcid.org/0000-0001-6120-7695
author: https://orcid.org/0000-0001-9011-5642
author: https://orcid.org/0000-0002-5865-8994
author: https://orcid.org/0000-0002-1220-9173
keywords: proteomics
keywords: Food Science
keywords: Forensics
keywords: phylogenetics
keywords: Ecology
keywords: mass spectrometry
keywords: metabolomics
programming language: CSS
programming language: Go
programming language: HTML
programming language: JavaScript
programming language: Shell
license:
  creative work: creativeWork
    name: MIT
reference publication: acs.jproteome.2c00457
reference publication: rcm.6162

https://orcid.org/0000-0001-6120-7695
type: Person
given name: Benjamin
family name: Neely
name: Benjamin Neely
role name: Collaborator
affiliation: Organization
  name: National Institute of Standards and Technology

https://orcid.org/0000-0001-9011-5642
type: Person
given name: Madhushri S.
family name: Varunjikar
name: Madhushri S. Varunjikar
role name: Tester & User
affiliation: Organization
  name: Institute of Marine Research

https://orcid.org/0000-0002-5865-8994
type: Person
given name: Magnus
family name: Palmblad
name: Magnus Palmblad
role name: Principal Investigator
affiliation: Organization
  name: Leiden University Medical Center

https://orcid.org/0000-0002-1220-9173
type: Person
given name: Rob
family name: Marissen
name: Rob Marissen
role name: Lead Developer
affiliation: Organization
  name: Leiden University Medical Center

acs.jproteome.2c00457
type: ScholarlyArticle
name: compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets
pagination: 514-519
url: https://doi.org/10.1021%2Facs.jproteome.2c00457

rcm.6162
type: ScholarlyArticle
name: Molecular phylogenetics by direct comparison of tandem mass spectra
pagination: 728-732
url: https://doi.org/10.1002%2Frcm.6162