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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.
14
mentions
2
contributors
What compareMS2 can do for you
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) for further processing
Keywords
Programming languages
License
- MIT
</>Source code
Participating organisations
Mentions
Journal articles
13- 1.Shotgun proteomics approaches for authentication, biological analyses, and allergen detection in feed and food-grade insect speciesAuthor(s): Madhushri S. Varunjikar, Ikram Belghit, Jennifer Gjerde, Magnus Palmblad, Eystein Oveland, Josef D. RasingerPublished in Food Control by Elsevier BV in 2022, page: 10888810.1016/j.foodcont.2022.108888
- 2.compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry DatasetsAuthor(s): Rob Marissen, Madhushri S. Varunjikar, Jeroen F. J. Laros, Josef D. Rasinger, Benjamin A. Neely, Magnus PalmbladPublished in Journal of Proteome Research by American Chemical Society (ACS) in 2022, page: 514-51910.1021/acs.jproteome.2c00457
- 3.Comparing novel shotgun DNA sequencing and state-of-the-art proteomics approaches for authentication of fish species in mixed samplesAuthor(s): Madhushri S. Varunjikar, Carlos Moreno-Ibarguen, Juan S. Andrade-Martinez, Hui-Shan Tung, Ikram Belghit, Magnus Palmblad, Pål A. Olsvik, Alejandro Reyes, Josef D. Rasinger, Kai K. LiePublished in Food Control by Elsevier BV in 2022, page: 10841710.1016/j.foodcont.2021.108417
- 4.Future feed control – Tracing banned bovine material in insect mealAuthor(s): I. Belghit, M. Varunjikar, M-C. Lecrenier, A. Steinhilber, A. Niedzwiecka, Y.V. Wang, M. Dieu, D. Azzollini, K. Lie, E-J. Lock, M.H.G. Berntssen, P. Renard, J. Zagon, O. Fumière, J.J.A. van Loon, T. Larsen, O. Poetz, A. Braeuning, M. Palmblad, J.D. RasingerPublished in Food Control by Elsevier BV in 2021, page: 10818310.1016/j.foodcont.2021.108183
- 5.Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of ProteomicsAuthor(s): Benjamin A. Neely, Magnus PalmbladPublished in Journal of Proteome Research by American Chemical Society (ACS) in 2021, page: 4640-464510.1021/acs.jproteome.1c00528
- 6.Palaeoproteomics of bird bones for taxonomic classificationAuthor(s): Ivo R Horn, Yvo Kenens, N Magnus Palmblad, Suzanne J van der Plas-Duivesteijn, Bram W Langeveld, Hanneke J M Meijer, Hans Dalebout, Rob J Marissen, Anja Fischer, F B Vincent Florens, Jonas Niemann, Kenneth F Rijsdijk, Anne S Schulp, Jeroen F J Laros, Barbara GravendeelPublished in Zoological Journal of the Linnean Society by Oxford University Press (OUP) in 2019, page: 650-66510.1093/zoolinnean/zlz012
- 7.Species-Specific Discrimination of Insect Meals for Aquafeeds by Direct Comparison of Tandem Mass SpectraAuthor(s): Ikram Belghit, Erik-Jan Lock, Olivier Fumière, Marie-Caroline Lecrenier, Patricia Renard, Marc Dieu, Marc H. G. Berntssen, Magnus Palmblad, Josef D. RasingerPublished in Animals by MDPI AG in 2019, page: 22210.3390/ani9050222
- 8.Differentiating samples and experimental protocols by direct comparison of tandem mass spectraAuthor(s): Suzanne J. van der Plas‐Duivesteijn, Tune Wulff, Oleg Klychnikov, Dana Ohana, Hans Dalebout, Peter A. van Veelen, Jeroen de Keijzer, Merel A. Nessen, Yuri E. M. van der Burgt, André M. Deelder, Magnus PalmbladPublished in Rapid Communications in Mass Spectrometry by Wiley in 2016, page: 731-73810.1002/rcm.7494
- 9.Identification of meat products by shotgun spectral matchingAuthor(s): D. Ohana, H. Dalebout, R.J. Marissen, T. Wulff, J. Bergquist, A.M. Deelder, M. PalmbladPublished in Food Chemistry by Elsevier BV in 2016, page: 28-3410.1016/j.foodchem.2016.01.138
- 10.Species and tissues specific differentiation of processed animal proteins in aquafeeds using proteomics toolsAuthor(s): J.D. Rasinger, H. Marbaix, M. Dieu, O. Fumière, S. Mauro, M. Palmblad, M. Raes, M.H.G. BerntssenPublished in Journal of Proteomics by Elsevier BV in 2016, page: 125-13110.1016/j.jprot.2016.05.036
- 11.Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library MatchingAuthor(s): Merel A. Nessen, Dennis J. van der Zwaan, Sander Grevers, Hans Dalebout, Martijn Staats, Esther Kok, Magnus PalmbladPublished in Journal of Agricultural and Food Chemistry by American Chemical Society (ACS) in 2016, page: 3669-367710.1021/acs.jafc.5b05322
- 12.Authentication of Fish Products by Large-Scale Comparison of Tandem Mass SpectraAuthor(s): Tune Wulff, Michael Engelbrecht Nielsen, André M. Deelder, Flemming Jessen, Magnus PalmbladPublished in Journal of Proteome Research by American Chemical Society (ACS) in 2013, page: 5253-525910.1021/pr4006525
- 13.Molecular phylogenetics by direct comparison of tandem mass spectraAuthor(s): Magnus Palmblad, André M. DeelderPublished in Rapid Communications in Mass Spectrometry by Wiley in 2012, page: 728-73210.1002/rcm.6162
Contributors
MP
Magnus Palmblad
American Chemical Society
RM
Rob Marissen
Leiden University Medical Center