Credentialed E. coli Cell Extract Kits

Credentialed E. coli Cell Extract Kits

Metabolomics generates large, complex datasets. Due to this complexity, it is challenging to assess method performance, to identify analytes, and to compare data across laboratories and experiments. The diversity of metabolite analytes and metabolomic study designs precludes the use of one or a few standards to address these challenging questions. A solution, developed by Patti and colleagues, is the credentialing protocol. This utilizes E. coli cell extracts and novel Credentialing software to discriminate features of biological origin from contaminants (e.g., plastic leachable, solvent impurities, carryover) and artifacts (e.g., informatic errors) without having to identify metabolite structures.

CIL is pleased to offer Credentialed E. coli Cell Extract Kits for untargeted metabolomic developments, which use E. coli as a representative complex biological sample. These kits are supplied as a solution, MSK-CRED-KIT, and as dried down, MSK-CRED-DD-KIT. They are designed to assist in optimizing methods for untargeted, metabolomic profiling studies (see references below for example applications).

Kit contents:

¹³C-labeled E. coli cell extract (dried down or 100 µL).
Unlabeled E. coli cell extract (dried down or 100 µL).
Document package (supplied via QR code). Package includes user manual, which contains instructions on solution/sample preparation and data analysis.

Resources

Credentialed E. coli Cell Extract Kits

Mixtures, Sets, and Kits for MS ‘Omics and MS/MS Screening

Stable Isotope Standards for Mass Spectrometry

Dr. Gary Patti's C&EN Webinar on Credentialing

Frequently Asked Questions

What types of optimizations or comparison could these MSK-CRED kits be used for?

Using an untargeted metabolomics platform, these kits could be used for performance comparison (e.g., column, instrument) or parameter optimization (e.g., instruments, informatics). The kits could also be used to rule out sources of peak contamination (e.g., materials arising from syringe, tubing, connections).

What is the procedure for extract reconstitution?

The dry extracts in MSK-CRED-DD-KIT should be reconstituted in 100 μL of ACN/H₂O (1:1, v/v) then sonicated (for 10 minutes) and centrifuged (e.g., for 15 minutes at 13,000 rpm and 4°C) before overnight incubation at 4ºC. This results in a clear solution. Aliquots of the ¹³C-labeled and unlabeled extracts should then be mixed (e.g., 1:2 and 1:1 v/v) and vortexed. Upon transfer to LC vials, the sample is ready for LC-MS or LC-MS/MS analysis.

Can the dried down extracts be reconstituted in alternate solvent ratios?

It is reasonable to alter the reconstitution recommendations of 1:1 v/v ACN:water. The recommended solvent ratio was chosen in an attempt to capture both water-soluble and lipid-soluble metabolites. Changing the ratio to increase ACN or water will increase the coverage of organic or water-soluble metabolites, respectively. The effectiveness of the credentialing approach, however, will not be affected by the solvent ratio employed.

How many sample runs will each kit allow?

Under typical LC-MS protocols (involves 5 μL injection; example provided in the user manual that is supplied with the kit), the extracts (both solution and dried down) enable 20 runs.

References

Sindelar, M.; Patti, G.J. 2020. Chemical discovery in the era of metabolomics. J Am Chem Soc, 142(20), 9097-9105. PMID: 32275430

Wang, L.; Naser, F.J.; Spalding, J.L.; et al. 2019. A protocol to compare methods for untargeted metabolomics. Methods Mol Biol, 1862, 1-15. PMID: 30315456

Spalding, J.L.; Naser, F.J.; Mahieu, N.G.; et al. 2018. Trace phosphate improves ZIC-pHILIC peak shape, sensitivity, and coverage for untargeted metabolomics. J Proteome Res, 17(10), 3537-3546. PMID: 30160483

Naser, F.J.; Mahieu, N.G.; Wang, L.; et al. 2018. Two complementary reversed-phase separations for comprehensive coverage of the semipolar and nonpolar metabolome. Anal Bioanal Chem, 410(4), 1287-1297. PMID: 29256075

Mahieu, N.G.; Patti, G.J. 2017. Systems-level annotation of a metabolomics data set reduces 25,000 features to fewer than 1,000 unique metabolites. Anal Chem, 89(19), 10397-10406. PMID: 28914531

Benton, H.P.; Ivanisevic, J.; Mahieu, N.G.; et al. 2015. Autonomous metabolomics for rapid metabolite identification in global profiling. Anal Chem, 87(2), 884-891. PMID: 25496351

Mahieu, N.G.; Huang, X.; Chen, Y.; et al. 2014. Credentialing features: a platform to benchmark and optimize untargeted metabolomic methods. Anal Chem, 86(19), 9583-9589. PMID: 25160088

Krista Backiel

Marketing Manager and Metabolomics Manager

Krista Backiel is responsible for managing and promoting products that are utilized in metabolomics and clinical/diagnostic MS. She spends a lot of her time developing new products to assist customers in their diverse research efforts.

Andrew Percy, PhD

Senior Applications Chemist – Mass Spectrometry

Dr. Andrew Percy is the Senior Applications Chemist for Mass Spectrometry and the MS ‘Omics Product Manager at CIL. His responsibilities minimally involve providing technical support, overseeing product development, identifying new product market opportunities, assisting in the analysis of product-related applications, and writing/reviewing marketing literature.