Literature DB >> 27306312

Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge.

Jody C May1, John A McLean1.   

Abstract

Hybrid analytical instrumentation constructed around mass spectrometry (MS) is becoming the preferred technique for addressing many grand challenges in science and medicine. From the omics sciences to drug discovery and synthetic biology, multidimensional separations based on MS provide the high peak capacity and high measurement throughput necessary to obtain large-scale measurements used to infer systems-level information. In this article, we describe multidimensional MS configurations as technologies that are big data drivers and review some new and emerging strategies for mining information from large-scale datasets. We discuss the information content that can be obtained from individual dimensions, as well as the unique information that can be derived by comparing different levels of data. Finally, we summarize some emerging data visualization strategies that seek to make highly dimensional datasets both accessible and comprehensible.

Entities:  

Keywords:  integrated omics sciences; mass defect analysis; metabolites; metabolomics; peak capacity; structural elucidation; systems biology

Year:  2016        PMID: 27306312      PMCID: PMC5763907          DOI: 10.1146/annurev-anchem-071015-041734

Source DB:  PubMed          Journal:  Annu Rev Anal Chem (Palo Alto Calif)        ISSN: 1936-1327            Impact factor:   10.745


  120 in total

1.  Three-dimensional imaging of lipids and metabolites in tissues by nanospray desorption electrospray ionization mass spectrometry.

Authors:  Ingela Lanekoff; Kristin Burnum-Johnson; Mathew Thomas; Jeeyeon Cha; Sudhansu K Dey; Pengxiang Yang; Maria C Prieto Conaway; Julia Laskin
Journal:  Anal Bioanal Chem       Date:  2014-11-14       Impact factor: 4.142

2.  Systems biology and new technologies enable predictive and preventative medicine.

Authors:  Leroy Hood; James R Heath; Michael E Phelps; Biaoyang Lin
Journal:  Science       Date:  2004-10-22       Impact factor: 47.728

3.  Assessing the peak capacity of IMS-IMS separations of tryptic peptide ions in He at 300 K.

Authors:  Samuel I Merenbloom; Brian C Bohrer; Stormy L Koeniger; David E Clemmer
Journal:  Anal Chem       Date:  2007-01-15       Impact factor: 6.986

4.  Extracting metabolite ions out of a matrix background by combined mass defect, neutral loss and isotope filtration.

Authors:  Filip Cuyckens; Rob Hurkmans; Jose M Castro-Perez; Laurent Leclercq; Russell J Mortishire-Smith
Journal:  Rapid Commun Mass Spectrom       Date:  2009-01       Impact factor: 2.419

5.  Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps.

Authors:  Cody R Goodwin; Brett C Covington; Dagmara K Derewacz; C Ruth McNees; John P Wikswo; John A McLean; Brian O Bachmann
Journal:  Chem Biol       Date:  2015-04-30

6.  Examining troughs in the mass distribution of all theoretically possible tryptic peptides.

Authors:  Alexey V Nefedov; Indranil Mitra; Allan R Brasier; Rovshan G Sadygov
Journal:  J Proteome Res       Date:  2011-08-09       Impact factor: 4.466

7.  Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics.

Authors:  Jesse D Canterbury; Xianhua Yi; Michael R Hoopmann; Michael J MacCoss
Journal:  Anal Chem       Date:  2008-08-12       Impact factor: 6.986

Review 8.  Analysis of tissue specimens by matrix-assisted laser desorption/ionization imaging mass spectrometry in biological and clinical research.

Authors:  Jeremy L Norris; Richard M Caprioli
Journal:  Chem Rev       Date:  2013-02-11       Impact factor: 60.622

9.  The Spectral Game: leveraging Open Data and crowdsourcing for education.

Authors:  Jean-Claude Bradley; Robert J Lancashire; Andrew Sid Lang; Antony J Williams
Journal:  J Cheminform       Date:  2009-06-26       Impact factor: 5.514

Review 10.  Bioinformatics: the next frontier of metabolomics.

Authors:  Caroline H Johnson; Julijana Ivanisevic; H Paul Benton; Gary Siuzdak
Journal:  Anal Chem       Date:  2014-11-20       Impact factor: 6.986

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  28 in total

1.  Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS.

Authors:  Pier-Luc Plante; Élina Francovic-Fontaine; Jody C May; John A McLean; Erin S Baker; François Laviolette; Mario Marchand; Jacques Corbeil
Journal:  Anal Chem       Date:  2019-04-01       Impact factor: 6.986

2.  Evaluating Separation Selectivity and Collision Cross Section Measurement Reproducibility in Helium, Nitrogen, Argon, and Carbon Dioxide Drift Gases for Drift Tube Ion Mobility-Mass Spectrometry.

Authors:  Caleb B Morris; Jody C May; Katrina L Leaptrot; John A McLean
Journal:  J Am Soc Mass Spectrom       Date:  2019-03-18       Impact factor: 3.109

Review 3.  Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites.

Authors:  Brett C Covington; John A McLean; Brian O Bachmann
Journal:  Nat Prod Rep       Date:  2017-01-04       Impact factor: 13.423

4.  Correlating Resolving Power, Resolution, and Collision Cross Section: Unifying Cross-Platform Assessment of Separation Efficiency in Ion Mobility Spectrometry.

Authors:  James N Dodds; Jody C May; John A McLean
Journal:  Anal Chem       Date:  2017-10-30       Impact factor: 6.986

5.  Discovery of Lipidome Alterations Following Traumatic Brain Injury via High-Resolution Metabolomics.

Authors:  Scott R Hogan; John H Phan; Melissa Alvarado-Velez; May Dongmei Wang; Ravi V Bellamkonda; Facundo M Fernández; Michelle C LaPlaca
Journal:  J Proteome Res       Date:  2018-04-27       Impact factor: 4.466

Review 6.  Fundamentals of Ion Mobility-Mass Spectrometry for the Analysis of Biomolecules.

Authors:  Caleb B Morris; James C Poland; Jody C May; John A McLean
Journal:  Methods Mol Biol       Date:  2020

7.  A Web Service Framework for Interactive Analysis of Metabolomics Data.

Authors:  Yaroslav Lyutvinskiy; Jeramie D Watrous; Mohit Jain; Roland Nilsson
Journal:  Anal Chem       Date:  2017-05-17       Impact factor: 6.986

Review 8.  Untargeted Metabolomics Strategies-Challenges and Emerging Directions.

Authors:  Alexandra C Schrimpe-Rutledge; Simona G Codreanu; Stacy D Sherrod; John A McLean
Journal:  J Am Soc Mass Spectrom       Date:  2016-09-13       Impact factor: 3.109

9.  Untargeted Molecular Discovery in Primary Metabolism: Collision Cross Section as a Molecular Descriptor in Ion Mobility-Mass Spectrometry.

Authors:  Charles M Nichols; James N Dodds; Bailey S Rose; Jaqueline A Picache; Caleb B Morris; Simona G Codreanu; Jody C May; Stacy D Sherrod; John A McLean
Journal:  Anal Chem       Date:  2018-11-30       Impact factor: 6.986

10.  An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements.

Authors:  Sarah M Stow; Tim J Causon; Xueyun Zheng; Ruwan T Kurulugama; Teresa Mairinger; Jody C May; Emma E Rennie; Erin S Baker; Richard D Smith; John A McLean; Stephan Hann; John C Fjeldsted
Journal:  Anal Chem       Date:  2017-08-16       Impact factor: 6.986

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