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

Boecker, Sebastian; Lipták, Zsuzsanna; Martin, Marcel; Pervukhin, Anton; Sudek, Henner

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.

Zeitschriftenaufsatz | Veröffentlicht | Englisch

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DOI

https://doi.org/10.1093/bioinformatics/btm631

Autor*in

Boecker, Sebastian; Lipták, Zsuzsanna^UniBi; Martin, Marcel^UniBi; Pervukhin, Anton; Sudek, Henner

Einrichtung

Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Institut für Bioinformatik

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

2008

Zeitschriftentitel

BIOINFORMATICS

Band

Ausgabe

Seite(n)

591-593

ISSN

1367-4803

eISSN

1460-2059

Page URI

https://pub.uni-bielefeld.de/record/1592737

Zitieren

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. https://doi.org/10.1093/bioinformatics/btm631

Boecker, Sebastian, Lipták, Zsuzsanna, Martin, Marcel, Pervukhin, Anton, and Sudek, Henner. 2008. “DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem”. BIOINFORMATICS 24 (4): 591-593.

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.

Daten bereitgestellt von European Bioinformatics Institute (EBI)

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.
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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