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An online peak extraction algorithm for ion mobility spectrometry data

Dominik Kopczynski, Sven Rahmann
2015 Algorithms for Molecular Biology  
Ion mobility (IM) spectrometry (IMS), coupled with multi-capillary columns (MCCs), has been gaining importance for biotechnological and medical applications because of its ability to detect and quantify  ...  We describe the different algorithmic steps in detail and evaluate the online method against state-of-the-art peak extraction methods.  ...  We are grateful to Jörg Ingo Baumbach for help with numerous questions and for providing datasets. We thank Max Wornowizki from subproject C3 for providing methodology for the first evaluation.  ... 
doi:10.1186/s13015-015-0045-5 pmid:26157473 pmcid:PMC4495807 fatcat:lpmupgljjvhflg4drozow4mnfi

An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data [chapter]

Dominik Kopczynski, Sven Rahmann
2014 Lecture Notes in Computer Science  
Ion mobility (IM) spectrometry (IMS), coupled with multi-capillary columns (MCCs), has been gaining importance for biotechnological and medical applications because of its ability to detect and quantify  ...  We describe the different algorithmic steps in detail and evaluate the online method against state-of-the-art peak extraction methods.  ...  We are grateful to Jörg Ingo Baumbach for help with numerous questions and for providing datasets. We thank Max Wornowizki from subproject C3 for providing methodology for the first evaluation.  ... 
doi:10.1007/978-3-662-44753-6_18 fatcat:tobf3wcijfd3pdqi4tmif2mlcy

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Jian Ma, Cameron P Casey, Xueyun Zheng, Yehia M Ibrahim, Christopher S Wilkins, Ryan S Renslow, Dennis G Thomas, Samuel H Payne, Matthew E Monroe, Richard D Smith, Justin G Teeguarden, Erin S Baker (+2 others)
2017 Bioinformatics  
Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for  ...  The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses.  ...  Given a list of empirical formulae for target molecules of interest, our algorithm analyzes the DTIMS-MS data for each target ion and extracts the arrival times at the peak centroids for each electric  ... 
doi:10.1093/bioinformatics/btx305 pmid:28505286 pmcid:PMC5860068 fatcat:33of3z43ezghniwxccsqq4od4y

DEIMoS: an open-source tool for processing high-dimensional mass spectrometry data [article]

Sean M. Colby, Christine H. Chang, Jessica L. Bade, Jamie R. Nunez, Madison R. Blumer, Daniel J. Orton, Kent J. Bloodsworth, Ernesto S. Nakayasu, Richard D. Smith, Yehia M. Ibrahim, Ryan S. Renslow, Thomas O. Metz
2021 arXiv   pre-print
We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass spectrometry data analysis  ...  Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation; algorithm implementations simultaneously utilize all dimensions to (i) offer greater separation between  ...  An Agilent 1100 Column Heater was used with a static temperature of 45°C. Ion mobility spectrometry-tandem mass spectrometry analysis was performed using an Agilent 6560 Ion Mobility LC/Q-TOF system.  ... 
arXiv:2112.03466v1 fatcat:zauyeydzqjht5kfyapplspggdu

Integration of Ion Mobility MSE after Fully Automated, Online, High-Resolution Liquid Extraction Surface Analysis Micro-Liquid Chromatography

Lieke Lamont, Mark Baumert, Nina Ogrinc Potočnik, Mark Allen, Rob Vreeken, Ron M. A. Heeren, Tiffany Porta
2017 Analytical Chemistry  
The platform integrates an online buffer exchange and washing step for removal of salts and other endogenous contamination that originates from local tissue extraction.  ...  We developed a comprehensive, fully automated online platform for high-resolution liquid extraction surface analysis (HR-LESA) followed by micro− liquid chromatography (LC) separation and a data-independent  ...  For this reason, an additional gas-phase IMS was added to the analytical workflow to increase the analytical content of the data. Ion Mobility Separation (IMS) of Isobaric Species.  ... 
doi:10.1021/acs.analchem.7b03512 pmid:28945354 pmcid:PMC5677252 fatcat:rb7kdycsqjanle5rfvrpxl7bai

Novel technologies for metabolomics: More for less

Paul Miggiels, Bert Wouters, Gerard J.P. van Westen, Anne-Charlotte Dubbelman, Thomas Hankemeier
2018 TrAC. Trends in analytical chemistry  
Recent trends include miniaturisation and automation of extraction techniques, online coupling to fast analysis methods including direct infusion ion mobility MS, integrated microfluidic devices, and sharing  ...  and standardizing metabolomics software and data.  ...  Likewise, we observe an increased use of ion mobility for ultra-fast separations.  ... 
doi:10.1016/j.trac.2018.11.021 fatcat:6s7wsogyd5fudjv5hzbk3yw3je

Optimised Desorption Electrospray Ionisation Mass Spectrometry Imaging (DESI-MSI) for the Analysis of Proteins/Peptides Directly from Tissue Sections on a Travelling Wave Ion Mobility Q-ToF

Mark W. Towers, Tamas Karancsi, Emrys A. Jones, Steven D. Pringle, Emmanuelle Claude
2018 Journal of the American Society for Mass Spectrometry  
Without the use of ion mobility separation prior to mass spectrometry analysis, only the most abundant charge series were observed.  ...  Desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) is typically known for the ionisation of small molecules such as lipids and metabolites, in singly charged form.  ...  The resulting spectra were summed to give an overall measure of the signal. Data were acquired using tandem ion mobility separation and oa-ToF mass spectrometry.  ... 
doi:10.1007/s13361-018-2049-0 pmid:30168053 fatcat:iw4h7pe23ra4raxcabgzopojqi

Effective Ion Mobility Peak Width as a New Isomeric Descriptor for the Untargeted Analysis of Complex Mixtures Using Ion Mobility-Mass Spectrometry

Mathilde Farenc, Benoit Paupy, Sabrina Marceau, Eleanor Riches, Carlos Afonso, Pierre Giusti
2017 Journal of the American Society for Mass Spectrometry  
Ion mobility coupled with mass spectrometry was proven to be an efficient way to characterize complex mixtures such as petroleum samples.  ...  This indicator is based on the full width at half maximum (FWHM) of the extracted ion mobility peak measured in millisecond or square angstrom that is corrected for instrumental factors such as ion diffusion  ...  With partially resolved signals it is possible to use a peak fitting algorithm to deconvolute ion mobility peaks.  ... 
doi:10.1007/s13361-017-1749-1 pmid:28721674 fatcat:pjiixxgphbbyvliu62zr7vhoqe

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

Hiroshi Tsugawa, Tomas Cajka, Tobias Kind, Yan Ma, Brendan Higgins, Kazutaka Ikeda, Mitsuhiro Kanazawa, Jean VanderGheynst, Oliver Fiehn, Masanori Arita
2015 Nature Methods  
Data-independent acquisition (DIA) in liquid chromatography tandem mass spectrometry (LC-MS/MS) provides more comprehensive untargeted acquisition of molecular data.  ...  For reversed phase LC-MS/MS, our program with an enriched LipidBlast library identified total 1,023 lipid compounds from nine algal strains to highlight their chemotaxonomic relationships.  ...  We also thank the Lipid MAPS consortium for providing us the lipid SDF files; ChemAxon for a free research license for the Marvin and JChem cheminformatics tools; Z. Tietel and N.  ... 
doi:10.1038/nmeth.3393 pmid:25938372 pmcid:PMC4449330 fatcat:shxo3x5z3rbivblf37iwkbcuua

A roadmap for the XCMS family of software solutions in metabolomics

Nathaniel G Mahieu, Jessica Lloyd Genenbacher, Gary J Patti
2016 Current Opinion in Chemical Biology  
The objective of this review is to provide an overview of the freely available bioinformatic solutions that are either based upon or are compatible with the algorithms in XCMS, which we broadly refer to  ...  These include CAMERA, credentialing, Warpgroup, metaXCMS, X 13 CMS, and XCMS Online.  ...  Acknowledgements GJP received financial support for this work from the National Institutes of Health Grants R01 ES022181 and L30 AG0 038036, as well as the Alfred P.  ... 
doi:10.1016/j.cbpa.2015.11.009 pmid:26673825 pmcid:PMC4831061 fatcat:gppt6zz3xvbslgp2och4gzkr4q

Intact protein bioanalysis by liquid chromatography – High-resolution mass spectrometry

Peter Bults, Baubek Spanov, Oladapo Olaleye, Nico C. van de Merbel, Rainer Bischoff
2019 Journal of chromatography. B  
Mass spectrometry and notably high-resolution mass spectrometry allows more specific detection of proteins based on extracted ion chromatograms (EICs) with narrow mass extraction windows (MEWs) (see later  ...  That is why further developments in both mass spectrometry (e.g. reducing the number of charges per protein ion by 'native' mass spectrometry) and algorithms are ongoing [99] .  ... 
doi:10.1016/j.jchromb.2019.01.032 fatcat:clsjrone5rdsvjpebi4tmb6kee

Trapped ion mobility spectrometry (TIMS) and parallel accumulation - serial fragmentation (PASEF) enable in-depth lipidomics from minimal sample amounts [article]

Catherine G Vasilopoulou, Karolina Sulek, Andreas-David Brunner, Ningombam Sanjib Meitei, Ulrike Schweiger-Hufnagel, Sven W. Meyer, Aiko Barsch, Matthias Mann, Florian Meier
2019 bioRxiv   pre-print
Here, we develop a high-sensitivity lipidomics workflow based on nanoflow liquid chromatography and trapped ion mobility spectrometry.  ...  Our study establishes PASEF in lipid analysis and paves the way for sensitive, ion mobility-enhanced lipidomics in four dimensions.  ...  Acknowledgements We thank our colleagues in the department of Proteomics and Signal Transduction for discussion and help, in particular D. Voytik, A.  ... 
doi:10.1101/654491 fatcat:ectkmbhqnfdupj3vz4zjbqes2q

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

Florian Meier, Andreas-David Brunner, Scarlet Koch, Heiner Koch, Markus Lubeck, Michael Krause, Niels Goedecke, Jens Decker, Thomas Kosinski, Melvin A. Park, Nicolai Bache, Ole Hoerning (+3 others)
2018 Molecular & Cellular Proteomics  
Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of its small size, low voltage requirements and high efficiency of ion utilization.  ...  It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation.  ...  Acknowledgments-We thank our colleagues in the department of Proteomics and Signal Transduction and at Bruker Bremen and Bruker Billerica for discussion and help, in particular Drs. P. Geyer and I.  ... 
doi:10.1074/mcp.tir118.000900 pmid:30385480 pmcid:PMC6283298 fatcat:bigogfzad5h53ozkamlstnf3am

Chemometrics for ion mobility spectrometry data: recent advances and future prospects

Ewa Szymańska, Antony N. Davies, Lutgarde M. C. Buydens
2016 The Analyst  
This is the first comprehensive review on chemometric techniques used in ion mobility spectrometry data analysis.  ...  Ewa Szymańska would like to thank Sanne van den Dikkenberg for her assistance in the literature search.  ...  Acknowledgements This research received funding from the Netherlands Organization for Scientific Research (NWO) in the framework of the Technology Area COAST, project 053.21.109.  ... 
doi:10.1039/c6an01008c pmid:27549384 fatcat:jvjsjsre2bgnthcuoykz7xpcp4

Structure/reaction directed analysis for LC-MS based untargeted analysis

Miao Yu, Mariola Olkowicz, Janusz Pawliszyn
2019 Analytica Chimica Acta  
Pawliszyn, Structure/reaction directed analysis for LC-MS based untargeted analysis, Analytica Chimica Acta, https://doi.  ...  To this end, such an analysis was also performed on raw peak data, without prior 537 application of the GlobalStd algorithm.  ...  Highlights -Algorithms were developed to reduce redundant peaks in metabolomics data profile -20% of the original peaks could stand for the major variances for data -Quantitative analysis could be performed  ... 
doi:10.1016/j.aca.2018.10.062 fatcat:nqrc7duwivf3lkajyfgvw775ai
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