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Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
2012
BMC Bioinformatics
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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
2018
Analytica Chimica Acta
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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
2005
Metabolomics
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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
2011
Computer applications in the biosciences : CABIOS
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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]
2018
bioRxiv
pre-print
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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
2009
Bioanalysis
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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
2008
Computer applications in the biosciences : CABIOS
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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]
2009
Information Technologies in Environmental Engineering
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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
2020
Journal of Separation Science
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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
2013
Computer applications in the biosciences : CABIOS
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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
2011
Talanta: The International Journal of Pure and Applied Analytical Chemistry
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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
2010
BMC Bioinformatics
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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
2021
Metabolites
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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
2012
Journal of Chromatography A
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, 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
2012
Journal of the American Society for Mass Spectrometry
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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
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