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ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

Nils Hoffmann, Jens Stoye
2009 Computer applications in the biosciences : CABIOS  
We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains.  ...  Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions.  ...  ACKNOWLEDGEMENTS The authors would like to thank Tony Watt for providing the example GC-MS data available for evaluation on the web site. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp343 pmid:19505941 pmcid:PMC2722998 fatcat:cikw7hvfe5f5jkwnd6zbo636ai

Generic Software Frameworks for GC-MS Based Metabolomics [chapter]

Nils Hoffmann, Jens Stoye
2012 Metabolomics  
We finally thank our students Mathias Wilhelm for his work on ChromA4D and Kai-Bernd Stadermann for his work on the RMI-based remote execution framework.  ...  and for kindly providing us with the datasets.  ...  ChromA ChromA is a configuration of Maltcms that includes preprocessing, in the form of mass binning, time-scale alignment and annotation of signal peaks found within the data, as well as visualizations  ... 
doi:10.5772/31224 fatcat:dqt23nueeje53mm23zmbohbu54

DIAlignR provides precise retention time alignment across distant runs in DIA and targeted proteomics [article]

Shubham Gupta, Sara Ahadi, Wenyu Zhou, Hannes L. Rost
2018 bioRxiv   pre-print
Here, we present a novel algorithm for retention time alignment of SWATH-MS data based on direct alignment of raw MS2 chromatograms using a hybrid dynamic programming approach.  ...  as the liquid chromatography column, all of which affect retention time (RT) reproducibility and successively performance of SWATH-MS data analysis.  ...  Combining peak-and chromatogram-based retention time alignment 24 algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics 30. Chambers, J. M., Hastie, T. J. & Others.  ... 
doi:10.1101/438309 fatcat:72xmvm4mljfankhjnoayifb36q

Chromaligner: a web server for chromatogram alignment

San-Yuan Wang, Tsung-Jung Ho, Ching-Hua Kuo, Yufeng J. Tseng
2010 Computer applications in the biosciences : CABIOS  
Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis  ...  It also provides alignments based on known component peaks to reach the best results for further chemometric analysis.  ...  Emilio Esposito for editing and the reviewers for their insightful comments and suggestions.  ... 
doi:10.1093/bioinformatics/btq337 pmid:20576623 fatcat:wpfuyyzcinc27c6ugvrdr2yojq

OpenMS – An open-source software framework for mass spectrometry

Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher
2008 BMC Bioinformatics  
Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics.  ...  Results: We present OpenMS, a software framework for rapid application development in mass spectrometry.  ...  Christian Huber (Saarland University, Germany) for providing the experimental data used for development and testing.  ... 
doi:10.1186/1471-2105-9-163 pmid:18366760 pmcid:PMC2311306 fatcat:ydzwiuwdhfff5k2xj4iaglslde

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools

Sean O'Callaghan, David P De Souza, Andrew Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia L Tull, Ute Roessner, Antony Bacic, Malcolm J McConville (+1 others)
2012 BMC Bioinformatics  
Gas chromatography-mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites.  ...  PyMS implements parallel processing for by-row and by-column data processing tasks based on Message Passing Interface (MPI), allowing processing to scale on multiple CPUs in distributed computing environments  ...  Background Gas chromatography (GC) coupled with mass spectrometry (MS) is frequently used in metabolomics [1] [2] [3] [4] [5] .  ... 
doi:10.1186/1471-2105-13-115 pmid:22647087 pmcid:PMC3533878 fatcat:3lgyx3we3bf5fcgp4ncsswkpaa

MeltDB: a software platform for the analysis and integration of metabolomics experiment data

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann
2008 Computer applications in the biosciences : CABIOS  
MeltDB is a web-based software platform for the analysis and annotation of datasets from metabolomics experiments.  ...  The newly developed system covers the process from raw data management to the visualization of results in a knowledge-based background and is integrated into the existing software platforms of genomics  ...  Gas chromatography -mass spectrometry (GC-MS) Gas chromatography-mass spectrometry (GC-MS) combines the features of gas chromatography and mass spectrometry to identify substances within a complex sample  ... 
doi:10.1093/bioinformatics/btn452 pmid:18765459 fatcat:6kraieexyvaq7hcx4fikyqg5gq

DIAlignR provides precise retention time alignment across distant runs in DIA and targeted proteomics

Shubham Gupta, Sara Ahadi, Wenyu Zhou, Hannes Rost
2019 Molecular & Cellular Proteomics  
such as the liquid chromatography column, all of which affect retention time (RT) reproducibility and, successively, performance of SWATH-MS data analysis.  ...  Here, we present a novel algorithm for RT alignment of SWATH-MS data based on direct alignment of raw MS2 chromatograms using a hybrid dynamic programming approach.  ...  We also thank Michael Brudno for valuable discussion on chromatogram alignment using dynamic programming.  ... 
doi:10.1074/mcp.tir118.001132 pmid:30705124 pmcid:PMC6442363 fatcat:fjqkx37eqnd7pocbxkzgbjquma

An Automated Time-Shift Alignment Algorithm Based on Discrete to Continuous Approach

Wajih Rhalem, Mourad Raji, Ahmed Hammouch, Jamal El Mhamdi
2019 Journal of Computer Science  
Dealing with the variation in retention time and time series is one of the most popular challenges in the field of analysing data obtained from biological experiments.  ...  The experimental results have shown good performance of the proposed algorithm that has been applied on different types of time series data.  ...  Acknowledgement We would like to thank the Technical Support Units for Scientific Research (UATRS) of the National Center for Scientific and Technical Research (CNRST) in Rabat, Morocco for providing the  ... 
doi:10.3844/jcssp.2019.463.474 fatcat:iytwsdcti5fihcvdyzik6dk7ru

Chemometric evaluation of Saccharomyces cerevisiae metabolic profiles using LC–MS

Mireia Farrés, Benjamí Piña, Romà Tauler
2014 Metabolomics  
modeling of liquid chromatographymass spectrometry data in Wold, S., Esbensen, K., & Geladi, P. (1987).  ...  of unintended stress effects based on a metabonomic study in Liquid chromatographymass spectrometry based global metab- tomato fruits after treatment with Carbofuran pesticide.  ... 
doi:10.1007/s11306-014-0689-z pmid:25598766 pmcid:PMC4289532 fatcat:wlunxfcai5fuxmpjsea6kw2coe

Signal enhancement for gradient reverse-phase high-performance liquid chromatography-electrospray ionization mass spectrometry analysis with trifluoroacetic and other strong acid modifiers by postcolumn addition of propionic acid and isopropanol

Frank E. Kuhlmann, Alex Apffel, Steven M. Fischer, Gerson Goldberg, Paul C. Goodley
1995 Journal of the American Society for Mass Spectrometry  
ionization mass spectrometry (ESI-MS).  ...  Signal enhancement is typically 10-50 times for peptides and other small basic molecules.  ...  lts'd.R longer retention times aRd sharper pea'ks '0m.' a sili.~a,; based reverse-phase coLumn.  ... 
doi:10.1016/1044-0305(95)00571-4 pmid:24214073 fatcat:5snnz4x4pzaljg3zncmr2akesy

CC1, a Novel Crenarchaeal DNA Binding Protein

X. Luo, U. Schwarz-Linek, C. H. Botting, R. Hensel, B. Siebers, M. F. White
2006 Journal of Bacteriology  
These properties are consistent with a role for CC1 as a crenarchaeal chromatin protein.  ...  We performed a biochemical screen for novel nucleic acid binding proteins present in cell extracts of T. tenax.  ...  We thank the MRC for funding C.H.B. Mass spectrometry at the University of St. Andrews is funded by the Wellcome Trust.  ... 
doi:10.1128/jb.01246-06 pmid:17085561 pmcid:PMC1797387 fatcat:vby6z47p35e3dhjrnl3qorqh5q

Gas chromatography‑time of flight/mass spectrometry‑based metabonomics of changes in the urinary metabolic profile in osteoarthritic rats

Hui Jiang, Jian Liu, Xiu‑Juan Qin, Yuan‑Yuan Chen, Jia‑Rong Gao, Mei Meng, Yuan Wang, Ting Wang
2018 Experimental and Therapeutic Medicine  
The aim of the present study was to explore changes in the urinary metabolic spectrum in rats with knee osteoarthritis, using gas chromatography-time of flight/mass spectrometry (GC-TOF/MS) to determine  ...  ., Shanghai, China) for providing help with data analysis.  ...  /mass spectrometry and gas chromatography-time of flight/mass spectrometry (GC-TOF/MS) (8) .  ... 
doi:10.3892/etm.2018.5788 pmid:29599826 pmcid:PMC5867455 fatcat:ju7bocbmbrgmjjeion5kmrrgcu

Comparison of the biochemical and molecular properties of myoglobins from three Biomphalaria species

Kádima N. Teixeira, Jamil S. Oliveira, Karyne N. Souza, Juliana de Moura, Cristiane A. Brito, Teofânia H.D.A. Vidigal, Alexandre M.C. Santos, Marcelo M. Santoro
2011 Biochemical Systematics and Ecology  
Data analysis showed that these proteins are monomers with the signature for the classic myoglobin fold and they are blocked in amino terminus probably by an acetyl group.  ...  Native (not recombinant) myoglobins of these two Biomphalaria species were purified and their experimental molecular mass (about 16 kDa) and pI (about (8.0) were provided.  ...  Two different retention times, referent to myoglobin, were obtained in reverse phase chromatography for the three species of mollusks; 34.27 s and 35.41 s, 34.37 s and 35.21 s, 34.12 s and 35.70 s for  ... 
doi:10.1016/j.bse.2011.04.006 fatcat:4zi55pcucvdzpngy44voiffzd4

Gas chromatographic technologies for the analysis of essential oils

Philip J Marriott, Robert Shellie, Charles Cornwell
2001 Journal of Chromatography A  
Clearly, today the analyst turns to chromatography as the provider of separation and then may supplement that with mass spectrometry to aid identification.  ...  Mass spectrometry will be included to the extent that it represents the hyphenation of choice for most analysts when analysing essential oils.  ...  Gas chromatography-mass spectrometry Gas chromatography-mass spectrometry has prob-4.3.  ... 
doi:10.1016/s0021-9673(01)01314-0 pmid:11760992 fatcat:7lu6pw7yuvdoxow2kybnzzakm4
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