DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem

Boecker S, Lipták Z, Martin M, Pervukhin A, Sudek H (2008)
BIOINFORMATICS 24(4): 591-593.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
We introduce DECOMP a tool that computes the sum formula of all molecules whose mass equals the input mass. This problem arises frequently in biochemistry and mass spectrometry (MS), when we know the molecular mass of a protein, DNA or metabolite fragment but have no other information. A closely related problem is known as the Money Changing Problem (MCP), where all masses are positive integers. Recently, efficient algorithms have been developed for the MCP, in which DECOMP applies to real-valued MS data. The excellent performance of this method on proteomic and metabolomic MS data has recently been demonstrated. DECOMP has an easy-to-use graphical interface, which caters for both types of users: those interested in solving MCP instances and those submitting MS data.
Erscheinungsjahr
Zeitschriftentitel
BIOINFORMATICS
Band
24
Zeitschriftennummer
4
Seite
591-593
ISSN
eISSN
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Boecker S, Lipták Z, Martin M, Pervukhin A, Sudek H. DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem. BIOINFORMATICS. 2008;24(4):591-593.
Boecker, S., Lipták, Z., Martin, M., Pervukhin, A., & Sudek, H. (2008). DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem. BIOINFORMATICS, 24(4), 591-593. doi:10.1093/bioinformatics/btm631
Boecker, S., Lipták, Z., Martin, M., Pervukhin, A., and Sudek, H. (2008). DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem. BIOINFORMATICS 24, 591-593.
Boecker, S., et al., 2008. DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem. BIOINFORMATICS, 24(4), p 591-593.
S. Boecker, et al., “DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem”, BIOINFORMATICS, vol. 24, 2008, pp. 591-593.
Boecker, S., Lipták, Z., Martin, M., Pervukhin, A., Sudek, H.: DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem. BIOINFORMATICS. 24, 591-593 (2008).
Boecker, Sebastian, Lipták, Zsuzsanna, Martin, Marcel, Pervukhin, Anton, and Sudek, Henner. “DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem”. BIOINFORMATICS 24.4 (2008): 591-593.

8 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C., J Cheminform 9(1), 2017
PMID: 29086040
Digging into the low molecular weight peptidome with the OligoNet web server.
Liu Y, Forcisi S, Lucio M, Harir M, Bahut F, Deleris-Bou M, Krieger-Weber S, Gougeon RD, Alexandre H, Schmitt-Kopplin P., Sci Rep 7(1), 2017
PMID: 28916823
Using R and Bioconductor for proteomics data analysis.
Gatto L, Christoforou A., Biochim Biophys Acta 1844(1 pt a), 2014
PMID: 23692960
Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.
Dührkop K, Hufsky F, Böcker S., Mass Spectrom (Tokyo) 3(spec iss 2), 2014
PMID: 26819880
Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways.
Cho K, Evans BS, Wood BM, Kumar R, Erb TJ, Warlick BP, Gerlt JA, Sweedler JV., Metabolomics 2014(august), 2014
PMID: 25705145
Computational mass spectrometry for small molecules.
Scheubert K, Hufsky F, Böcker S., J Cheminform 5(1), 2013
PMID: 23453222
Molecular Formula Identification with SIRIUS.
Dührkop K, Scheubert K, Böcker S., Metabolites 3(2), 2013
PMID: 24958003
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation.
Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, Elnakady YA, Müller R, Böcker S, Huber CG, Kohlbacher O., Electrophoresis 30(21), 2009
PMID: 19862751

8 References

Daten bereitgestellt von Europe PubMed Central.

A computer program for the computation of the molecular formula
Fürst, Chemometrics and Intelligent Laboratory Systems 5(4), 1989
Determination of oligonucleotide composition from mass spectrometrically measured molecular weight
Pomerantz, Journal of the American Society for Mass Spectrometry 4(3), 1993
Determination of the empirical formula of peptides by fast atom bombardment mass spectrometry.
Bertrand MJ, Thibault P, Evans MJ, Zidarov D., Biomed. Environ. Mass Spectrom. 14(6), 1987
PMID: 2955829
Multistage Cutting Stock Problems of Two and More Dimensions
Gilmore, Operations Research 13(1), 1965

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