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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  
Here, we present an easyto-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid, reducing processing time from days to hours.  ...  Taverna workflow and command line tool are provided for remote processing of local user data. Availability: online data processing service is available at  ...  TAVERNA WORKFLOW AND COMMAND LINE OPTION The web user interface provides a convenient easy-to-use access to the high-throughput Warp2D LC-MS time alignment service.  ... 
doi:10.1093/bioinformatics/btr094 pmid:21349866 fatcat:ljqlt3qtvbditcty2dgonyhouq

Bioinformatics Tools for Metabolomic Data Processing and Analysis Using Untargeted Liquid Chromatography Coupled With Mass Spectrometry

Andrei G. Lazar, Florina Romanciuc, Mihai Adrian Socaciu, Carmen Socaciu
2015 Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca. Animal Science and Biotechnologies  
This review presents updated information about different high-throughput analytical techniques and data acquisition software (1-2), the pre-processing of data, converted to specific matrices, further processed  ...  New software is available for data conversion, pre-processing, alignment algorithms, bucketing, normalization, underlying the challenges and comparisons with international data bases.  ...  As a summary for data processing and analysis, Table 2 includes a list of the most important tools available for LC/MS metabolomics spectral processing and data analysis Tab.2.  ... 
doi:10.15835/buasvmcn-asb:11536 fatcat:f4kid3lzcbghlp3xtgfococyi4

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report

Russell P. Bowler, Chris H. Wendt, Michael B. Fessler, Matthew W. Foster, Rachel S. Kelly, Jessica Lasky-Su, Angela J. Rogers, Kathleen A. Stringer, Brent W. Winston
2017 Annals of the American Thoracic Society  
The goal of this workshop was to convene, for the first time, relevant experts in lung proteomics and metabolomics to discuss and overcome specific challenges in these fields that are unique to the lung  ...  and challenges of lung-specific biological specimens for metabolomic and proteomic analysis; (3) the diverse informatics approaches and databases unique to metabolomics and proteomics, with special emphasis  ...  Special thanks to Aubrey Shoe, National Jewish Health, for administrative assistance, and ATS administrative staff Breana Portelli and Kimberly Lawrence.  ... 
doi:10.1513/annalsats.201710-770ws pmid:29192815 pmcid:PMC5946579 fatcat:pjzokf6ej5dlfdxfzztttunnca

Analytical Methods for Detection of Plant Metabolomes Changes in Response to Biotic and Abiotic Stresses

Anna Piasecka, Piotr Kachlicki, Maciej Stobiecki
2019 International Journal of Molecular Sciences  
Moreover, advanced integration of metabolomics data with these obtained on other omics levels: genome, transcriptome and proteome should be carried out.  ...  Such a holistic approach would bring us closer to understanding biochemical and physiological processes of the cell and whole plant interacting with the environment and further apply these observations  ...  Joint aligner developed for MZmine2 and implemented also in MS-Dial were used in plant metabolomics [103, 114] ) An extended method for alignment data with larger retention time drift and MS/MS spectrum  ... 
doi:10.3390/ijms20020379 fatcat:xhwo2gbg55cavh6zvgbhnygnd4

Generic Software Frameworks for GC-MS Based Metabolomics [chapter]

Nils Hoffmann, Jens Stoye
2012 Metabolomics  
Acknowledgements We would like to thank Manuela Meyer at the Center for Biotechnology (CeBiTec), Bielefeld University, Germany, for the preparation of the GC-MS samples used in this work.  ...  We furthermore thank Denise Schöfbeck and Rainer Schumacher, Center for Analytical Chemistry, IFA Tulln, University of Natural Resources and Life Sciences, Vienna, Austria, for measuring those samples  ...  of unaligned and aligned data from GC-MS and LC-MS experiments.  ... 
doi:10.5772/31224 fatcat:dqt23nueeje53mm23zmbohbu54

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  
Finally, the review discusses the current state and trends in high throughput data processing and analysis solutions for users with little bioinformatics knowledge.  ...  Label-free quantitative LC-MS profiling of complex body fluids has become an important analytical tool for biomarker and biological knowledge discovery in the past decade.  ...  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

The metaRbolomics Toolbox in Bioconductor and beyond

Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski (+7 others)
2019 Metabolites  
Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system.  ...  This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation  ...  For the pre-processing of LC-MS and GC-MS data, xcms is widely used.  ... 
doi:10.3390/metabo9100200 pmid:31548506 pmcid:PMC6835268 fatcat:3b2gnq6qdrcfbcq6hewgoobdce

Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis

Masahiro Sugimoto, Masato Kawakami, Martin Robert, Tomoyoshi Soga, Masaru Tomita
2012 Current Bioinformatics  
This paper provides a state-of-the-art overview of the data processing tools available, and reviews a collection of recent reports on the topic.  ...  Thus, bioinformatics tools are essential for the efficient processing of huge datasets, the characterization of the detected signals, and to align multiple datasets and their features.  ...  We thank Akira Oikawa at the Riken Plant Science Center and Fumio Matsuta at Kobe University for fruitful discussions.  ... 
doi:10.2174/157489312799304431 pmid:22438836 pmcid:PMC3299976 fatcat:au2ydk6yb5crpivhhkfgny6y7u

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  
The automation of the sample acquisition and subsequent analysis in high throughput instruments that are capable of measuring metabolites is posing a challenge on the necessary systematic storage and computational  ...  and integrated storage and analysis of data obtained from metabolomics experiments.  ...  Furthermore, with the availability of multiple alignments, the processing of high-throughput metabolomics data is simplified.  ... 
doi:10.1093/bioinformatics/btn452 pmid:18765459 fatcat:6kraieexyvaq7hcx4fikyqg5gq

Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines [article]

Yasset Perez-Riverol, Pablo Moreno
2019 bioRxiv   pre-print
In this paper we overview the key steps of metabolomic and proteomics data processing including main tools and software use to perform the data analysis.  ...  Finally, we introduced to the proteomics and metabolomics communities a new approach for reproducible and large-scale data analysis based on BioContainers and two of the most popular workflows environments  ...  Computational proteomics and metabolomics have been dominated by desktop and monolithic software for the past decades, which hampered high throughput analysis in High-Performance Computing systems (HPCS  ... 
doi:10.1101/604413 fatcat:doy6yj6g3jhjzi5kn3bzaimt3m

Online Metabolomics Databases and Pipelines [chapter]

Adam J.
2012 Metabolomics  
Description: A study design database for GC/MS metabolomics experiments. Species: Plant species Reference data: Provides raw and processed GC/MS data for download together with metadata.  ...  Noteworthy features: Metabolite detections are searchable by species and species are searchable by metabolite detections. Modes of access: Search, browse and download.  ...  Public databases of "Accurate Mass / retention Time (AMT) tags" are playing increasingly important roles in peptide identification in LC-MS proteomics (Hagiwara et al., 2010) .  ... 
doi:10.5772/31021 fatcat:7nkgmwx72nesleacrrulcrwf4a

msCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies

Berend Hoekman, Rainer Breitling, Frank Suits, Rainer Bischoff, Peter Horvatovich
2012 Molecular & Cellular Proteomics  
Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.015974, 1-13, 2012. LC-MS is a well established analysis technique in the field of proteomics and metabolomics (1-5).  ...  scientists to determine which combination of modules provides the most accurate processing for their particular LC-MS data sets.  ...  Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.015974, 1-13, 2012. LC-MS is a well established analysis technique in the field of proteomics and metabolomics (1) (2) (3) (4) (5) .  ... 
doi:10.1074/mcp.m111.015974 pmid:22318370 pmcid:PMC3433919 fatcat:akvgjui5bvbdbfx6xil3vyrmz4

Single-Cell Proteomics: The Critical Role of Nanotechnology

Carlota Arias-Hidalgo, Pablo Juanes-Velasco, Alicia Landeira-Viñuela, Marina L. García-Vaquero, Enrique Montalvillo, Rafael Góngora, Ángela-Patricia Hernández, Manuel Fuentes
2022 International Journal of Molecular Sciences  
In addition, nanotechnology has enabled high-throughput proteomics analysis, which have required the improvement of software tools, such as DART-ID or DO-MS, which are also fundamental for addressing key  ...  Mass spectrometry (MS)-based proteomics (e.g., SCoPE-MS and SCoPE2) can be used as a non-targeted method to detect molecules across hundreds of individual cells.  ...  Data-driven Alignment of Retention Times for IDentification (DART-ID) Leverage reproducible retention times to increase peptide identifications in LC-MS/MS proteomics.  ... 
doi:10.3390/ijms23126707 pmid:35743151 pmcid:PMC9224324 fatcat:pkhyyftz5fbllc77mtbwxujimu

"A novel paradigm for optimal mass feature peak picking in large scale LC-MS datasets using the 'isopair': isoLock, autoCredential and anovAlign" [article]

Allen Hubbard, Louis Connelly, Shrikaar Kambhampati, Brad Evans, Ivan Baxter
2021 bioRxiv   pre-print
This software suite opens a new era for enhanced accuracy and increased throughput for untargeted metabolomics.  ...  Liquid chromatography mass spectrometry (LC-MS), a popular method to implement untargeted metabolomics, identifies metabolites via combined mass/charge (m/z) and retention time as mass features.  ...  resource in the form of a large and high-quality dataset..  ... 
doi:10.1101/2021.12.05.471237 fatcat:srecwrgunbel3dzutfzrkxb6ia

Metabolomics to Characterize Adaptive and Signaling Responses in Legume Crops under Abiotic Stresses

Paula C. P. Bueno, Norberto P. Lopes
2020 ACS Omega  
In addition, metabolomics is a powerful tool for the evaluation and selection of wild specimens with desirable traits that can be used in the development of improved new cultivars.  ...  Legume species are an important source of protein and other nutrients for human and livestock consumption, playing a central role in food security.  ...  Joachim Kopka and Alexander Erban from Max-Planck Institute of Molecular Plant Physiology for the fruitful discussions and support.  ... 
doi:10.1021/acsomega.9b03668 pmid:32039310 pmcid:PMC7003242 fatcat:d3apiuxwjvgbvlpyayrjd4fi5u
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