Analytical strategies for LC–MS-based targeted metabolomics

Lu, Wenyun; Bennett, Bryson D.; Rabinowitz, Joshua D.

doi:10.1016/j.jchromb.2008.04.031

Cited by 427 publications

(314 citation statements)

References 72 publications

Supporting

Mentioning

307

Contrasting

Unclassified

Order By: Relevance

“…This analysis was complemented with LC coupled by ESI (negative mode) to a Thermo Scientific TSQ Quantum triple-quadrupole mass spectrometer operating in single-reaction monitoring mode (50). Amino acids were derivatized with benzyl chloroformate before their quantitation by negative-mode LC-ESI-MS/MS (51).…”

Section: Methodsmentioning

confidence: 99%

Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state

Babbitt

Altenhofen

Cobbold

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

153

242

View full text Add to dashboard Cite

The human malaria parasite Plasmodium falciparum is auxotrophic for most amino acids. Its amino acid needs are met largely through the degradation of host erythrocyte hemoglobin; however the parasite must acquire isoleucine exogenously, because this amino acid is not present in adult human hemoglobin. We report that when isoleucine is withdrawn from the culture medium of intraerythrocytic P. falciparum, the parasite slows its metabolism and progresses through its developmental cycle at a reduced rate. Isoleucine-starved parasites remain viable for 72 h and resume rapid growth upon resupplementation. Protein degradation during starvation is important for maintenance of this hibernatory state. Microarray analysis of starved parasites revealed a 60% decrease in the rate of progression through the normal transcriptional program but no other apparent stress response. Plasmodium parasites do not possess a TOR nutrient-sensing pathway and have only a rudimentary amino acid starvation-sensing eukaryotic initiation factor 2α (eIF2α) stress response. Isoleucine deprivation results in GCN2-mediated phosphorylation of eIF2α, but kinase-knockout clones still are able to hibernate and recover, indicating that this pathway does not directly promote survival during isoleucine starvation. We conclude that P. falciparum, in the absence of canonical eukaryotic nutrient stress-response pathways, can cope with an inconsistent bloodstream amino acid supply by hibernating and waiting for more nutrient to be provided.protease | artemesinin | autophagy

show abstract

Section: Methodsmentioning

confidence: 99%

Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state

Babbitt

Altenhofen

Cobbold

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

153

242

View full text Add to dashboard Cite

show abstract

“…Samples were analyzed for watersoluble metabolites and saponified fatty acids by a stand-alone orbitrap mass spectrometer (Exactive) operating in negative ion mode and coupled to reversed-phase ion-pairing chromatography as described previously (23,24). In addition, confirmatory measurements of water-soluble metabolites were acquired with a TSQ Quantum Discovery triple-quadrupole mass spectrometer operating in negative ion, multiple-reaction monitoring mode coupled to reversed-phase ion-pairing chromatography as described (25). Data were analyzed using the MAVEN software suite (26).…”

Section: Methodsmentioning

confidence: 99%

Fatty Acid Labeling from Glutamine in Hypoxia Can Be Explained by Isotope Exchange without Net Reductive Isocitrate Dehydrogenase (IDH) Flux

Fan

Kamphorst

Rabinowitz

et al. 2013

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Background: Cancer cells in hypoxia were claimed to rely on reductive isocitrate dehydrogenase (IDH) for lipogenesis based on increased isotopic labeling of fatty acids from glutamine. Results: Oxidative IDH flux persists in hypoxia, whereas acetyl-CoA demand drops. Conclusion: Reductive IDH flux may not be a net contributor to acetyl-CoA production. Significance: Isotopic label incorporation is indicative of flux, although not necessarily of net flux.

show abstract

“…The platform utilizes hydrophilic interaction chromatography (HILIC) at pH ϭ 9.0 (31,32). 254 unique polar metabolites from 285 SRM scans were targeted from a single 16-min experiment without chromatographic scheduling.…”

mentioning

confidence: 99%

Metabolomics of Human Cerebrospinal Fluid Identifies Signatures of Malignant Glioma

Locasale

Melman

Song

et al. 2012

Molecular & Cellular Proteomics

100

View full text Add to dashboard Cite

Cerebrospinal fluid is routinely collected for the diagnosis and monitoring of patients with neurological malignancies. However, little is known as to how its constituents may change in a patient when presented with a malignant glioma. Here, we used a targeted mass-spectrometry based metabolomics platform using selected reaction monitoring with positive/negative switching and profiled the relative levels of over 124 polar metabolites present in patient cerebrospinal fluid. We analyzed the metabolic profiles from 10 patients presenting malignant gliomas and seven control patients that did not present malignancy to test whether a small sample size could provide statistically significant signatures. We carried out multiple unbiased forms of classification using a series of unsupervised techniques and identified metabolic signatures that distinguish malignant glioma patients from the control patients. One subtype identified contained metabolites enriched in citric acid cycle components. Newly diagnosed patients segregated into a different subtype and exhibited low levels of metabolites involved in tryptophan metabolism, which may indicate the absence of an inflammatory signature. Together our results provide the first global assessment of the polar metabolic composition in cerebrospinal fluid that accompanies malignancy, and demonstrate that data obtained from high throughput mass spectrometry technology may have suitable predictive capabilities for the

show abstract

Analytical strategies for LC–MS-based targeted metabolomics

Cited by 427 publications

References 72 publications

Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state

Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state

Fatty Acid Labeling from Glutamine in Hypoxia Can Be Explained by Isotope Exchange without Net Reductive Isocitrate Dehydrogenase (IDH) Flux

Metabolomics of Human Cerebrospinal Fluid Identifies Signatures of Malignant Glioma

Contact Info

Product

Resources

About