References
- Achterberg T., Scip: Solving constraint integer programs. Mathematical Programming Computation, 1(1):1–41, July 2009.
- 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.
- Blazewicz J., Hammer P.L., Lukasiak P., Predicting secondary structures of proteins, IEEE Engineering in Medicine and Biology, 24, pp.88-94, 2005.
- Bocker S., Liptak Z.. A Fast and Simple Algorithm for the Money Changing Problem. Algorithmica, 48(4):413–432, 2007.
- 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.
- Borowski M., 2011, Models and algorithms for peptide sequence identification, Wydawnictwo NAKOM, Poznan Monographs in Computing and Its Applications (Edition 1, Volume 14), 2011.
- DiMaggio P.A., Floudas C.A., De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization, Analytical Chemistry, 2007
- Gross J.H.. Mass Spectrometry. Springer Berlin Heidelberg, 2011.
- Hong Y., Li S., Ye Y., Tang H., FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectra, bioRxiv, 2024
- 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.
- Kuehl D., Wang Y., The role of spectral accuracy in mass spectrometry, Spectroscopy Supplements Special Issues 04/01, 2007.
- 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.
- 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.
- 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
- McNaught A. D., Wilkinson A. IUPAC. Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”). Blackwell Scientific Publications, Oxford, 1997.
- 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.
- Neumann, Steen, Anton Pervukhin and Sebastian Böcker, Mass decomposition with the Rdisop package, Chemistry, Physics, 2006, 2008, 2009.
- Patiny L., Borel A.. ChemCalc: a building block for tomorrow’s chemical infrastructure. J Chem Inf Model, 53(5):1223–1228, May 2013.
- 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
- Remes et al., The Role of Spectral Accuracy in Mass Spectrometry, Chromatography Online, 2007.
- Silberring J., Kraj A., Drabik A. Proteomika i metabolomika. Wydawnictwo Uniwersytetu Warszawskiego, Warszawa, 2010.
- Silberring J., Kraj A. Proteomika. Wydział Chemii Uniwersytetu Jagiellońskiego, Kraków, 2004.