Algorithm for Determining the Sum Formula of Metabolites from Mass Spectrometry Spectra

[1] Achterberg T., Scip: Solving constraint integer programs. Mathematical Programming Computation, 1(1):1–41, July 2009. Search in Google Scholar

[2] Achterberg T., Berthold T., Koch T., Wolter K., Constraint integer programming: A new approach to integrate CP and MIP. Lecture Notes in Computer Science, 5015:6–20, 2008. Search in Google Scholar

[3] Blazewicz J., Hammer P.L., Lukasiak P., Predicting secondary structures of proteins, IEEE Engineering in Medicine and Biology, 24, pp.88-94, 2005. Search in Google Scholar

[4] Bocker S., Liptak Z.. A Fast and Simple Algorithm for the Money Changing Problem. Algorithmica, 48(4):413–432, 2007. Search in Google Scholar

[5] Bocker S., Liptak Z., Martin M., Pervukhin A., Sudek H.. DECOMP–from interpreting Mass Spectrometry peaks to solving the Money Changing Problem. Bioinformatics, 24(4):591–593, Feb 2008. Search in Google Scholar

[6] Borowski M., 2011, Models and algorithms for peptide sequence identification, Wydawnictwo NAKOM, Poznan Monographs in Computing and Its Applications (Edition 1, Volume 14), 2011. Search in Google Scholar

[7] DiMaggio P.A., Floudas C.A., De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization, Analytical Chemistry, 2007 Search in Google Scholar

[8] Gross J.H.. Mass Spectrometry. Springer Berlin Heidelberg, 2011. Search in Google Scholar

[9] Hong Y., Li S., Ye Y., Tang H., FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectra, bioRxiv, 2024 Search in Google Scholar

[10] Kind T., Fiehn O.: Metabolomic database annotations via query of elemental compositions. Mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics, 7(1), 2006, 1–10. Search in Google Scholar

[11] Kuehl D., Wang Y., The role of spectral accuracy in mass spectrometry, Spectroscopy Supplements Special Issues 04/01, 2007. Search in Google Scholar

[12] Lukasiak P., Blazewicz J., Milostan M., Some operations research methods for analyzing protein sequences and structures, Annals of Operations Research, 175, pp. 9-35, 2010. Search in Google Scholar

[13] Marczak Ł., Znajdek-Awiżeń P., Bylka W. The use of mass spectrometric techniques to differentiate isobaric and isomeric flavonoid conjugates from axyris amaranthoides. Molecules, 2016, 21(9):1229. Search in Google Scholar

[14] Marczak L., Idkowiak J., Tracz J., Stobiecki M., Perek B., Kostka-Jeziorny K., Tykarski A., Wanic-Kossowska M., Borowski M., Osuch M., Formanowicz D. and Luczak M., Mass Spectrometry-Based Lipidomics Reveals Differential Changes in the Accumulated Lipid Classes in Chronic Kidney Disease, Metabolites, 11(5):275, April 2021, DOI: 10.3390/metabo11050275 Search in Google Scholar

[15] McNaught A. D., Wilkinson A. IUPAC. Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”). Blackwell Scientific Publications, Oxford, 1997. Search in Google Scholar

[16] Meringer M., Reinker S., Zhang J., Muller A.. MS/MS Data Improves Automated Determination Molecular Formulas by Mass Spectrometry. MATCH Communications in Mathematical and Computer Chemistry, 65(2):259–290, June 2011. Search in Google Scholar

[17] Neumann, Steen, Anton Pervukhin and Sebastian Böcker, Mass decomposition with the Rdisop package, Chemistry, Physics, 2006, 2008, 2009. Search in Google Scholar

[18] Patiny L., Borel A.. ChemCalc: a building block for tomorrow’s chemical infrastructure. J Chem Inf Model, 53(5):1223–1228, May 2013. Search in Google Scholar

[19] Pluskal t., Uehara T., Yanagida M., Highly Accurate Chemical Formula Prediction Tool Utilizing High-Resolution Mass Spectra, MS/MS Fragmentation, Heuristic Rules, and Isotope Pattern Matching, Analytical Chemistry, 2012 Search in Google Scholar

[20] Remes et al., The Role of Spectral Accuracy in Mass Spectrometry, Chromatography Online, 2007. Search in Google Scholar

[21] Silberring J., Kraj A., Drabik A. Proteomika i metabolomika. Wydawnictwo Uniwersytetu Warszawskiego, Warszawa, 2010. Search in Google Scholar

[22] Silberring J., Kraj A. Proteomika. Wydział Chemii Uniwersytetu Jagiellońskiego, Kraków, 2004. Search in Google Scholar