Filters








1,436 Hits in 8.0 sec

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus, Jens Stoye
2012 BMC Bioinformatics  
Results: In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE)  ...  Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning  ...  Acknowledgements We acknowledge support of the publication fee by Deutsche Forschungsgemeinschaft and the Open Access Publication Funds of Bielefeld University. Author details  ... 
doi:10.1186/1471-2105-13-214 pmid:22920415 pmcid:PMC3546004 fatcat:3kjadmdqszchtju3ulwwtu3mbe

Tutorial: Correction of shifts in single-stage LC-MS(/MS) data

Vikram Mitra, Age K. Smilde, Rainer Bischoff, Péter Horvatovich
2018 Analytica Chimica Acta  
We thanks the comments and detailed discussion with Frank Suits researcher at IBM Watson Center.  ...  and provide a retention time transformation function, that corrects for monotonic retention time shifts and aligns LC-MS(/MS) datasets.  ...  Retention time correction algorithms can be classified in many ways such as: i) type of data and MS1 map dimensions used for the alignment, such as using the complete MS1 map, total ion or base peak chromatograms  ... 
doi:10.1016/j.aca.2017.09.039 pmid:29254573 fatcat:nmgax7hj4bg6pitgx5zt3s3h4i

A non-directed approach to the differential analysis of multiple LC–MS-derived metabolic profiles

O. Vorst, C. H. R. de Vos, A. Lommen, R. V. Staps, R. G. F. Visser, R. J. Bino, R. D. Hall
2005 Metabolomics  
Specifically-designed software has made it possible to combine all mass peaks on the basis of retention time and m/z values only, without prior identification, to produce a data matrix output which can  ...  As the most widely used technologies are all based on mass spectrometry (e.g.  ...  Acknowledgments We would like to thank Chris Maliepaard for valuable discussion.  ... 
doi:10.1007/s11306-005-4432-7 fatcat:jqltvyksbrdodk36scznh7urbi

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data

Isthiaq Ahmad, Frank Suits, Berend Hoekman, Morris A. Swertz, Heorhiy Byelas, Martijn Dijkstra, Rob Hooft, Dmitry Katsubo, Bas van Breukelen, Rainer Bischoff, Peter Horvatovich
2011 Computer applications in the biosciences : CABIOS  
This service provides the warping function, the sample chromatogram peak list with adjusted retention times and normalized quality scores based on the sum of overlapping peak volume of all peaks.  ...  Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and sample peak lists to correct misleading peak shifts.  ...  BACKGROUND Retention time alignment to correct non-linear retention time shifts (Podwojski et al., 2009 ) between different chromatograms is a crucial step in the processing of label-free liquid chromatography  ... 
doi:10.1093/bioinformatics/btr094 pmid:21349866 fatcat:ljqlt3qtvbditcty2dgonyhouq

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.  ...  The algorithm does not impose a chronological order of elution and allows for alignment of elution-order swapped peaks.  ...  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

Simple data-reduction method for high-resolution LC–MS data in metabolomics

RA Scheltema, S Decuypere, JC Dujardin, DG Watson, RC Jansen, R Breitling
2009 Bioanalysis  
The algorithm iterates through the 149 list of mass chromatogram sets by first selecting the most intense mass chromatogram set. 150 The retention time of this mass chromatogram set (i.e., the mean retention  ...  Before the procedure starts, mass chromatograms have 314 been extracted, aligned and combined (a peak set contains mass chromatograms from different mass spectra 315 in the data set corresponding to the  ... 
doi:10.4155/bio.09.146 pmid:21083103 fatcat:sbodyr552zd7nhwoommh2fmmcu

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.  ...  Comprehensive analysis and visualization features of metabolomics datasets are offered to the community through a web-based user interface.  ...  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

Analysing chromatographic data using data mining to monitor petroleum content in water [chapter]

Geoffrey Holmes, Dale Fletcher, Peter Reutemann, Eibe Frank
2009 Information Technologies in Environmental Engineering  
and correlation coefficients-to offer the potential for significantly reducing the time spent by analysts on this task.  ...  Chromatographic techniques, typically using gas or liquid chromatography coupled with mass spectrometry, allow an analyst to detect a vast array of compounds-potentially in the order of thousands.  ...  Hill Laboratories for their support.  ... 
doi:10.1007/978-3-540-88351-7_21 dblp:conf/itee/HolmesFRF09 fatcat:mishncgkwvcihibtexxtds3foi

Recent applications of chemometrics in one- and two-dimensional chromatography

Tijmen S. Bos, Wouter C. Knol, Stef R.A. Molenaar, Leon E. Niezen, Peter J. Schoenmakers, Govert W. Somsen, Bob W.J. Pirok
2020 Journal of Separation Science  
In this contribution, the requirement for chemometric tools is explained and the latest developments in approaches for (pre-)processing and analyzing data arising from one- and two-dimensional chromatography  ...  The proliferation of increasingly more sophisticated analytical separation systems, often incorporating increasingly more powerful detection techniques, such as high-resolution mass spectrometry, causes  ...  ., and L.N., acknowledge the UNMATCHED project, which is supported by BASF, DSM and Nouryon, and receives funding from the Netherlands Organization for Scientific Research (NWO) in the framework of the  ... 
doi:10.1002/jssc.202000011 pmid:32096604 fatcat:upxgzqbnfnfhfemknvy2gkypiq

BiPACE 2D—graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry

Nils Hoffmann, Mathias Wilhelm, Anja Doebbe, Karsten Niehaus, Jens Stoye
2013 Computer applications in the biosciences : CABIOS  
Results: We describe BIPACE 2D, an automated algorithm for retention time alignment of peaks from 2D gas chromatography-mass spectrometry experiments and evaluate it on three previously published datasets  ...  experimental protocol, peak-detection results and manually curated multiple peak alignment for future comparability with newly developed algorithms.  ...  ACKNOWLEDGMENTS The authors would like to thank the reviewers for their valuable comments and suggestions.  ... 
doi:10.1093/bioinformatics/btt738 pmid:24363380 fatcat:i2xyulfd6vhknhrhc363qah6i4

Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC–MS for biomarker discovery

Christin Christin, Rainer Bischoff, Péter Horvatovich
2011 Talanta: The International Journal of Pure and Applied Analytical Chemistry  
Accurate processing, statistical analysis and validation of acquired data diversified by the different types of mass spectrometers, mass spectrometer parameter settings and applied sample preparation steps  ...  Special emphasis is devoted to quality control methods, performance assessment of complete workflows and algorithms of individual modules.  ...  Acknowledgements This work was part of the Bioassist and BioRange programs of the Netherlands Bioinformatics Centre (NBIC) and Gaining Momentum Initiatives of NBIC and the Netherlands Proteomics Center  ... 
doi:10.1016/j.talanta.2010.10.029 pmid:21215856 fatcat:crgg275t7vf2hpgwz2vfqewxvi

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

Tomáš Pluskal, Sandra Castillo, Alejandro Villar-Briones, Matej Orešič
2010 BMC Bioinformatics  
alignment based on the random sample consensus (RANSAC) algorithm.  ...  The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms.  ...  We also thank the Okinawa Institute of Science and Technology Promotion Corporation for providing the funding and Mitsuhiro Yanagida for supporting the MZmine 2 development in his laboratory.  ... 
doi:10.1186/1471-2105-11-395 pmid:20650010 pmcid:PMC2918584 fatcat:tumlwbaaongode65emcdm5arru

Separation of Chromatographic Co-Eluted Compounds by Clustering and by Functional Data Analysis

Aneta Sawikowska, Anna Piasecka, Piotr Kachlicki, Paweł Krajewski
2021 Metabolites  
First, in both methods, data are normalized by the mass of sample, the baseline is removed, retention time alignment is conducted, and detection of peaks is performed.  ...  In this paper, two computational methods of separating peaks, applied, for the first time, to large chromatographic datasets, are described, compared, and experimentally validated.  ...  Surma, and T. Adamski from the Institute of Plant Genetics, Polish Academy of Sciences, for plant material.  ... 
doi:10.3390/metabo11040214 pmid:33807374 fatcat:ovs6zwnymja5dphge3bt2qubx4

Features for non-targeted cross-sample analysis with comprehensive two-dimensional chromatography

Stephen E. Reichenbach, Xue Tian, Chiara Cordero, Qingping Tao
2012 Journal of Chromatography A  
, and peak-region feature analysis.  ...  Comprehensive two-dimensional chromatography is a powerful technology for separating complex samples and so is well suited for non-targeted cross-sample analysis.  ...  National Science Foundation under Award Number IIP-1013180 and by the Nebraska Center for Energy Sciences Research.  ... 
doi:10.1016/j.chroma.2011.07.046 pmid:21855071 fatcat:hlwo6goc25cstjvitcmgichbye

Retention Time Alignment of LC/MS Data by a Divide-and-Conquer Algorithm

Zhongqi Zhang
2012 Journal of the American Society for Mass Spectrometry  
Liquid chromatography-mass spectrometry (LC/MS) has become the method of choice for characterizing complex mixtures.  ...  This article describes a simple pairwise iterative retention time alignment algorithm, based on the divide-and-conquer approach, for alignment of ion features detected in LC/MS experiments.  ...  Acknowledgment The author thanks Jason Richardson and Bhavana Shah for collecting some of the data to test the algorithm, and Pavel Bondarenko for helpful discussions during the development of the algorithm  ... 
doi:10.1007/s13361-011-0334-2 pmid:22298290 fatcat:lnv6se4hk5b4naltfy2hqd5bri
« Previous Showing results 1 — 15 out of 1,436 results