MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
TLDR
A new generation of a popular open-source data processing toolbox, MZmine 2 is introduced, suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.Abstract:
Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list 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. MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/
. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.read more
Citations
More filters
Journal ArticleDOI
Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought.
Albert Rivas-Ubach,Jordi Sardans,José Antonio Hódar,Joan Garcia-Porta,Alex Guenther,Ljiljana Paša-Tolić,Michal Oravec,Otmar Urban,Josep Peñuelas +8 more
TL;DR: The metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada, in summer and winter and exposed to folivory by the pine processionary moth, provided crucial insights into how iberica populations would respond to the predicted conditions of climate change under an increased defoliation in the Mediterranean Basin.
Journal ArticleDOI
Annotation and quantification of N-acyl homoserine lactones implied in bacterial quorum sensing by supercritical-fluid chromatography coupled with high-resolution mass spectrometry.
Thi Phuong Thuy Hoang,Morgane Barthélemy,Raphaël Lami,Didier Stien,Véronique Eparvier,David Touboul +5 more
TL;DR: A method for quantification of N-acyl homoserine lactones (AHLs), signaling molecules responsible for cell-to-cell communication initially discovered in bacteria, by SFC coupled with high-resolution mass spectrometry (HRMS) was developed and applied to study AHL production by one Gram-negative endophytic bacterium.
Journal ArticleDOI
Lipid Annotation by Combination of UHPLC-HRMS (MS), Molecular Networking, and Retention Time Prediction: Application to a Lipidomic Study of In Vitro Models of Dry Eye Disease.
Romain Magny,Romain Magny,Anne Regazzetti,Karima Kessal,Grégory Genta-Jouve,Grégory Genta-Jouve,Christophe Baudouin,Stéphane Mélik-Parsadaniantz,Françoise Brignole-Baudouin,Françoise Brignole-Baudouin,Olivier Laprévote,Nicolas Auzeil +11 more
TL;DR: This lipidomic study highlighted changes in 54 lipids following HO exposure of corneal cells, some of them being involved in inflammatory responses and appears as a suitable and robust tool for the discovery of lipids involved in relevant biological processes.
Journal ArticleDOI
Molecular Networking Reveals Serpentinine-Related Bisindole Alkaloids from Picralima nitida, a Previously Well-Investigated Species.
Charlotte Fox Alcover,Guillaume Bernadat,Faustin Aka Kabran,Pierre Le Pogam,Karine Leblanc,Alexander E. Fox Ramos,Jean-François Gallard,Elisabeth Mouray,Philippe Grellier,Erwan Poupon,Mehdi A. Beniddir +10 more
TL;DR: Five new monoterpene indole alkaloids, including four serpentinine-related bisindoles and one alstonine derivative monomer, have been isolated from the aerial parts of Picralima nitida and their structures were elucidated by analysis of their HRMS and NMR spectroscopic data.
Posted ContentDOI
Comparative molecular and immunoregulatory analysis of extracellular vesicles from Candida albicans and Candida auris
Daniel Zamith-Miranda,Heino M. Heyman,Sneha P. Couvillion,Radames J. B. Cordero,Marcio L. Rodrigues,Marcio L. Rodrigues,Leonardo Nimrichter,Arturo Casadevall,Rafaela F. Amatuzzi,Lysangela R. Alves,Ernesto S. Nakayasu,Joshua D. Nosanchuk +11 more
TL;DR: This work carried out a comparative molecular characterization of C. auris and C. albicans EVs and evaluated their capacity to modulate effector mechanisms of host immune defense, finding that C. Auris released EVs with payloads that were strikingly different from EVs released by C.Albicans.
References
More filters
Journal ArticleDOI
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
Journal ArticleDOI
Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography
TL;DR: New results are derived on the minimum number of landmarks needed to obtain a solution, and algorithms are presented for computing these minimum-landmark solutions in closed form that provide the basis for an automatic system that can solve the Location Determination Problem under difficult viewing.
Journal ArticleDOI
Probability-based protein identification by searching sequence databases using mass spectrometry data.
TL;DR: A new computer program, Mascot, is presented, which integrates all three types of search for protein identification by searching a sequence database using mass spectrometry data, and the scoring algorithm is probability based.
Journal ArticleDOI
Locally Weighted Regression: An Approach to Regression Analysis by Local Fitting
TL;DR: Locally weighted regression as discussed by the authors is a way of estimating a regression surface through a multivariate smoothing procedure, fitting a function of the independent variables locally and in a moving fashion analogous to how a moving average is computed for a time series.
Journal ArticleDOI
METLIN: a metabolite mass spectral database.
Colin A. Smith,Grace O'Maille,Elizabeth J. Want,Chuan Qin,Sunia A. Trauger,Theodore R. Brandon,Darlene E. Custodio,Ruben Abagyan,Gary Siuzdak +8 more
TL;DR: METLIN includes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrumetry (MS/MS) Spectra, and LC/MS data.
Related Papers (5)
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Mingxun Wang,Jeremy Carver,Vanessa V. Phelan,Laura M. Sanchez,Neha Garg,Yao Peng,Don D. Nguyen,Jeramie D. Watrous,Clifford A. Kapono,Tal Luzzatto-Knaan,Carla Porto,Amina Bouslimani,Alexey V. Melnik,Michael J. Meehan,Wei-Ting Liu,Max Crüsemann,Paul D. Boudreau,Eduardo Esquenazi,Mario Sandoval-Calderón,Roland D. Kersten,Laura A. Pace,Robert A. Quinn,Katherine R. Duncan,Cheng-Chih Hsu,Dimitrios J. Floros,Ronnie G. Gavilan,Karin Kleigrewe,Trent R. Northen,Rachel J. Dutton,Delphine Parrot,Erin E. Carlson,Bertrand Aigle,Charlotte Frydenlund Michelsen,Lars Jelsbak,Christian Sohlenkamp,Pavel A. Pevzner,Anna Edlund,Anna Edlund,Jeffrey S. McLean,Jeffrey S. McLean,Jörn Piel,Brian T. Murphy,Lena Gerwick,Chih-Chuang Liaw,Yu-Liang Yang,Hans-Ulrich Humpf,Maria Maansson,Robert A. Keyzers,Amy C. Sims,Andrew R. Johnson,Ashley M. Sidebottom,Brian E. Sedio,Andreas Klitgaard,Charles B. Larson,Charles B. Larson,Cristopher A. Boya P.,Daniel Torres-Mendoza,David Gonzalez,Denise Brentan Silva,Denise Brentan Silva,Lucas Miranda Marques,Daniel P. Demarque,Egle Pociute,Ellis C. O’Neill,Enora Briand,Enora Briand,Eric J. N. Helfrich,Eve A. Granatosky,Evgenia Glukhov,Florian Ryffel,Hailey Houson,Hosein Mohimani,Jenan J. Kharbush,Yi Zeng,Julia A. Vorholt,Kenji L. Kurita,Pep Charusanti,Kerry L. McPhail,Kristian Fog Nielsen,Lisa Vuong,Maryam Elfeki,Matthew F. Traxler,Niclas Engene,Nobuhiro Koyama,Oliver B. Vining,Ralph S. Baric,Ricardo Pianta Rodrigues da Silva,Samantha J. Mascuch,Sophie Tomasi,Stefan Jenkins,Venkat R. Macherla,Thomas Hoffman,Vinayak Agarwal,Philip G. Williams,Jingqui Dai,Ram P. Neupane,Joshua R. Gurr,Andrés M. C. Rodríguez,Anne Lamsa,Chen Zhang,Kathleen Dorrestein,Brendan M. Duggan,Jehad Almaliti,Pierre-Marie Allard,Prasad Phapale,Louis-Félix Nothias,Theodore Alexandrov,Marc Litaudon,Jean-Luc Wolfender,Jennifer E. Kyle,Thomas O. Metz,Tyler Peryea,Dac-Trung Nguyen,Danielle VanLeer,Paul Shinn,Ajit Jadhav,Rolf Müller,Katrina M. Waters,Wenyuan Shi,Xueting Liu,Lixin Zhang,Rob Knight,Paul R. Jensen,Bernhard O. Palsson,Kit Pogliano,Roger G. Linington,Marcelino Gutiérrez,Norberto Peporine Lopes,William H. Gerwick,William H. Gerwick,Bradley S. Moore,Bradley S. Moore,Pieter C. Dorrestein,Pieter C. Dorrestein,Nuno Bandeira,Nuno Bandeira +135 more
Proposed minimum reporting standards for chemical analysis
Lloyd W. Sumner,Alexander Amberg,Dave Barrett,Michael H. Beale,Richard D. Beger,Clare A. Daykin,Teresa W.-M. Fan,Oliver Fiehn,Royston Goodacre,Julian L. Griffin,Thomas Hankemeier,Nigel Hardy,James M. Harnly,Richard M. Higashi,Joachim Kopka,Andrew N. Lane,John C. Lindon,Philip J. Marriott,Andrew W. Nicholls,Michael D. Reily,John J. Thaden,Mark R. Viant +21 more
A cross-platform toolkit for mass spectrometry and proteomics
Matthew C. Chambers,Brendan MacLean,Robert Burke,Dario Amodei,Daniel Ruderman,Steffen Neumann,Laurent Gatto,Bernd Fischer,Brian S. Pratt,Jarrett D. Egertson,Katherine Hoff,Darren Kessner,Natalie Tasman,Nicholas J. Shulman,Barbara Frewen,Tahmina A Baker,Mi-Youn Brusniak,Christopher Paulse,David M. Creasy,Lisa Flashner,Kian Kani,Chris Moulding,Sean L. Seymour,Lydia M. Nuwaysir,Brent Lefebvre,Frank E. Kuhlmann,Joe Roark,Paape Rainer,Suckau Detlev,Tina Hemenway,Andreas Huhmer,James I. Langridge,Brian Connolly,Trey Chadick,Krisztina Holly,Josh Eckels,Eric W. Deutsch,Robert L. Moritz,Jonathan E. Katz,David B. Agus,Michael J. MacCoss,David L. Tabb,Parag Mallick,Parag Mallick +43 more