Get started
337 commitsLast commit ≈ 1 month ago3 stars1 fork
Ctrl K
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
</>Source code
Participating organisations
Mentions
Journal articles
13- 1.Author(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
- 2.Author(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
- 3.Author(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.Author(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.Author(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.Author(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.Author(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.Author(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
- 9.Author(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
- 10.Author(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
- 11.Author(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
- 12.Author(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.Author(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