Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry

Han, Jun; Danell, Ryan M.; Patel, Jayanti R; Gumerov, Dmitry R.; Scarlett, Cameron O.; Speir, J. Paul; Parker, Carol E.; Rusyn, Ivan; Zeisel, Steven H.; Borchers, Christoph H.

doi:10.1007/s11306-008-0104-8

Cited by 136 publications

(112 citation statements)

References 41 publications

Supporting

Mentioning

107

Contrasting

Unclassified

Order By: Relevance

“…Raw mass spectrometry data were processed using a customdeveloped software package as described elsewhere (10). First, raw mass spectra acquired from each sample group were batch processed using a home-written VBA script within the instrument vendor's data analysis software, DataAnalysis, to do automatic internal mass calibration with the reference masses of the spiked calibration standards and a known contaminant, N-butylbenzensulfonamide.…”

Section: Direct Infusion (Di)-ft-icr-msmentioning

confidence: 99%

Metabolomics Reveals Phospholipids as Important Nutrient Sources during Salmonella Growth in Bile In Vitro and In Vivo

et al. 2011

Self Cite

View full text Add to dashboard Cite

During the colonization of hosts, bacterial pathogens are presented with many challenges that must be overcome for colonization to occur successfully. This requires the bacterial sensing of the surroundings and adaptation to the conditions encountered. One of the major impediments to the pathogen colonization of the mammalian gastrointestinal tract is the antibacterial action of bile. Salmonella enterica serovar Typhimurium has specific mechanisms involved in resistance to bile. Additionally, Salmonella can successfully multiply in bile, using it as a source of nutrients. This accomplishment is highly relevant to pathogenesis, as Salmonella colonizes the gallbladder of hosts, where it can be carried asymptomatically and promote further host spread and transmission. To gain insights into the mechanisms used by Salmonella to grow in bile, we studied the changes elicited by Salmonella in the chemical composition of bile during growth in vitro and in vivo through a metabolomics approach. Our data suggest that phospholipids are an important source of carbon and energy for Salmonella during growth in the laboratory as well as during gallbladder infections of mice. Further studies in this area will generate a better understanding of how Salmonella exploits this generally hostile environment for its own benefit.

show abstract

Section: Direct Infusion (Di)-ft-icr-msmentioning

confidence: 99%

Metabolomics Reveals Phospholipids as Important Nutrient Sources during Salmonella Growth in Bile In Vitro and In Vivo

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…These ESI calibrant signals allow for internal mass calibration to provide high mass accuracy with mass error of <0.5 ppm 38 . As the ESI signal of the standard "ES Tuning Mix" solution can be an order of magnitude stronger than the MALDI signals of the analytes from the tissue, the ESI-derived calibrant signals must be attenuated.…”

Section: Representative Resultsmentioning

confidence: 99%

“…When conducting MALDI MSI experiments, initial identification of the detected analytes is usually based on metabolome database searching of the measured accurate masses which are usually only available when a high resolution instrument is used 38 . The dual ESI/MALDI ion source on the Apex-Qe 12-Tesla hybrid quadrupole-FTICR mass spectrometer allows for the addition of ESI-generated signals for use as the internal mass calibrant peaks to each MALDI mass spectrum, without affecting the MALDI desorption/ionization process.…”

Section: Discussionmentioning

confidence: 99%

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Han

Borchers

2013

JoVE

Self Cite

View full text Add to dashboard Cite

Mass spectrometry imaging (MSI) determines the spatial localization and distribution patterns of compounds on the surface of a tissue section, mainly using MALDI (matrix assisted laser desorption/ionization)-based analytical techniques. New matrices for small-molecule MSI, which can improve the analysis of low-molecular weight (MW) compounds, are needed. These matrices should provide increased analyte signals while decreasing MALDI background signals. In addition, the use of ultrahigh-resolution instruments, such as Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, has the ability to resolve analyte signals from matrix signals, and this can partially overcome many problems associated with the background originating from the MALDI matrix. The reduction in the intensities of the metastable matrix clusters by FTICR MS can also help to overcome some of the interferences associated with matrix peaks on other instruments. High-resolution instruments such as the FTICR mass spectrometers are advantageous as they can produce distribution patterns of many compounds simultaneously while still providing confidence in chemical identifications. Dithranol (DT; 1,8-dihydroxy-9,10-dihydroanthracen-9-one) has previously been reported as a MALDI matrix for tissue imaging. In this work, a protocol for the use of DT for MALDI imaging of endogenous lipids from the surfaces of mammalian tissue sections, by positive-ion MALDI-MS, on an ultrahigh-resolution hybrid quadrupole FTICR instrument has been provided. Video LinkThe video component of this article can be found at

show abstract

“…Kütle spektrometrisinin kullanımında bir diğer yaklaşım ise numunede bulunan metabolitlerin tamamının ayrılmadan kütle spektrometrisine verilmesidir. Özellikle yüksek ayrım gücüne (>1,000,000) ve kesinliğe (< 1 ppm) sahip Fourier Transform Kütle Spektrometrisi (FTMS) cihazları bu iş için kullanıldığında tatmin edici sonuçlar alınabilmektedir 28,29 . FTMS' in metabolomik çalışmalarda rutin kullanımına en büyük engel şu an için yüksek maliyeti ve dolayısıyla seyrek kullanımıdır 16 .…”

Section: Dedeksiyon Metodları Kütle Spektrometrisi (Ms)unclassified

Metabolomik Çalışmalarda Yazılım ve Veritabanı Desteği: LC-MS Verilerinin Değerlendirilmesinde XCMS Kullanımı

Çelebi̇er¹

2014

Arşiv Kaynak Tarama Dergisi

View full text Add to dashboard Cite

Metabolome is the complete set of small-molecule metabolites to be found in a cell or a single organism. Metabolomics is the scientific study to determine and identify the chemicals in metabolome with advanced analytical techniques. Nowadays, the elucidation of the molecular mechanism of any disease with genome analysis and proteome analysis is not sufficient. Instead of these, a holistic assessment including metabolomic studies provides rational and accurate results. Metabolite levels in an organism are associated with the cellular functions. Thus, determination of the metabolite amounts identifies the phenotype of a cell or tissue related with the genetic and some other variations. Even though, the analysis of metabolites for medical diagnosis and therapy have been performed for a long time, the studies to improve the analysis methods for metabolite profiling are recently increased. The application of metabolomics includes the identification of biomarkers, enzyme-substract interactions, drug-activity studies, metabolic pathway analysis and some other studies related with the system biology. The preprocessing and computing of the data obtained from LC-MS, GC-MS, CE-MS and NMR for metabolite profiling are helpful for preventing from time consuming manual data analysis processes and possible random errors on profiling period. In addition, such preprocesses allow us to identify low amount of metabolites which are not possible to be analyzed by manual processing. Therefore, the usage of software and databases for this purpose could not be ignored. In this study, it is briefly presented the software and database used on metabolomics and it is evaluated the capability of these software on metabolite profiling. Particularly, the performance of one of the most popular software called XCMS on the evaluation of LC-MS results for metabolomics was overviewed. In the

show abstract

Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry

Cited by 136 publications

References 41 publications

Metabolomics Reveals Phospholipids as Important Nutrient Sources during Salmonella Growth in Bile In Vitro and In Vivo

Metabolomics Reveals Phospholipids as Important Nutrient Sources during Salmonella Growth in Bile In Vitro and In Vivo

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Metabolomik Çalışmalarda Yazılım ve Veritabanı Desteği: LC-MS Verilerinin Değerlendirilmesinde XCMS Kullanımı

Contact Info

Product

Resources

About