A Web Service Framework for Interactive Analysis of Metabolomics Data

Analytical Chemistry
Yaroslav LyutvinskiyRoland Nilsson

Abstract

Analyzing mass spectrometry-based metabolomics data presents a major challenge to metabolism researchers, as it requires downloading and processing large data volumes through complex "pipelines", even in cases where only a single metabolite or peak is of interest. This presents a significant hurdle for data sharing, reanalysis, or meta-analysis of existing data sets, whether locally stored or available from public repositories. Here we introduce mzAccess, a software system that provides interactive, online access to primary mass spectrometry data in real-time via a Web service protocol, circumventing the need for bulk data processing. mzAccess allows querying instrument data for spectra, chromatograms, or two-dimensional MZ-RT areas in either profile or centroid modes through a simple, uniform interface that is independent of vendor or instrument type. Using a cache mechanism, mzAccess achieves response times in the millisecond range for typical liquid chromatography-mass spectrometry (LC-MS) peaks, enabling real-time browsing of large data sets with hundreds or even thousands of samples. By simplifying access to metabolite data, we hope that this system will help enable data sharing and reanalysis in the metabolomics field.

References

Jan 13, 2006·Therapeutic Drug Monitoring·Colin A SmithGary Siuzdak
May 1, 2007·Journal of Chromatography. a·Mikko Katajamaa, Matej Oresic
Dec 4, 2010·Science·Steven L McKnight
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Nov 30, 2013·Mass Spectrometry Reviews·Christophe JunotFrançois Bécher
Jan 9, 2014·Analytical Chemistry·Xiaojing HuangGary J Patti
Nov 2, 2014·Nucleic Acids Research·Nikolay KolesnikovAlvis Brazma
Dec 17, 2014·Molecular & Cellular Proteomics : MCP·David BouyssiéBernard Monsarrat
Jun 17, 2016·Annual Review of Analytical Chemistry·Jody C May, John A McLean
Aug 31, 2016·Nature Methods·Hannes L RöstOliver Kohlbacher

❮ Previous
Next ❯

Citations

Jan 3, 2018·Electrophoresis·Biswapriya B Misra
Oct 6, 2020·Cell Cycle·Irena RociRoland Nilsson
Nov 30, 2020·Metabolomics : Official Journal of the Metabolomic Society·Irena RociRoland Nilsson

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.