TruQuant Yeast Extract Semi-targeted QC Workflow Kit

The use of stable isotopes (as internal standards) is not a new thing, but using a 95% U-13C yeast extract internal standard  brings a lot to the table.

The QC Workflow kit contains dilute-and-shoot uniquely labeled yeast extract for use as an internal standard in quantitative MS-based quantitative profiling studies. Yeast is an ideal internal standard because it contains 100s of key primary metabolites including sugars, coenzymes, nucleotides, organic acids,  amino acids, peptides and polyamines.

Uses
  • Semi-targeted, LC-MS-based analysis
  • Ion suppression correction and sample normalization
  • Accurate metabolite ID and quantitation
  • Applicable to numerous sample matrices
  • Method and instrument QC
  • Biomarker discovery

Here at IROA Technologies, our metabolite yeast extract QC Workflow Kit simplifies the analysis for our clients. We provide cost-efficient internal metabolite standards as well as metabolite libraries to achieve reproducible results and make metabolomics easier.  We utilize the most advanced technology and internal measurement systems in an effort to reduce noise, variability, and ion suppression to deliver accurate and reproducible datasets.

Advantages of the unique 95% U-13C label

    • Automated through the use of ClusterFinder software
    • Labeled peaks easily found using software algorithms and their unlabeled counterparts in any sample matrix are identified and quantitated
    • 100s of metabolite peaks in the yeast extract have been well characterized by LC-MS-MS and incorporated into ClusterFinder
    • Improves metabolite identification
    • Through the use of the 95% U-13C internal standards ClusterFinder can correct for ion suppression and normalize samples
    • Built-in measurement of day-to-day (QA/QC) platform reproducibility
    • Workflow and Software only $200 (90 samples)!

See below for a list of compounds in the yeast internal standard.

In short, the Workflow is a high-quality quantitation system that utilizes two (2) complex Internal Standards to make accurate measurements of several hundred metabolites simultaneously in experimental samples and measure day-to-day (QA/QC) platform reproducibility.

Materials

  1. IROA LONG-TERM REFERENCE STANDARD – IROA-LTRS (paired 1:1 mixture of labeled U-5% and – 95% U-13C metabolites): The LTRS is analyzed every 10 samples for QC and used to build a triply redundant dictionary (library) of RT, m/z and physical characteristics using ClusterFinder software.
  2. IROA INTERNAL STANDARD – IROA-IS (labeled 95% U-13C metabolites): – spike into experimental samples and use as a yardstick in which to QUANTIFY all biochemicals in the sample relative to their counterparts in the IROA-LTRS. Even if analyzed on a different chromatographic system, results can be equated using dictionary because of the IROA-IS. Experimental compounds may have different RTs but will exhibit the same mass and physical characteristics.
  3. CLUSTERFINDER SOFTWARE

TruQuant Yeast Extract Semi-targeted QC Workflow 3 step process

  1. LC-MS analysis of experimental samples with IROA-IS.  Inject IROA-LTRS periodically i.e. 10 sample intervals, as QC Standard to account for fluctuations in mass and retention time drift.
  2. Generate “dictionary” of RT, m/z, formula and physical characteristics from the analysis of IROA-LTRS using ClusterFinder software.
  3. ClusterFinder software and dictionary identifies/quantitates, suppression corrects and normalizes compounds in experimental samples.

Summary of Benefits of the Yeast Extract Semi-targeted Workflow

  1. Daily instrument QA/QC.
  2. Economical – $200 for 90 samples
  3. No false data; removal of artifactual peaks.
  4. Accurate compound formula ID for MS alone; complete ID with addition of SWATH, or IM.
  5. Corrects for all source ionization losses  for significantly better quantitation.
  6. Normalizes samples to a universal standard for complete comparability.
  7. Yeast metabolites have been characterized by several LC-MS methods and incorporated into ClusterFinder software.
  8. ClusterFinder software solution builds libraries, IDs/quantitates compounds, corrects for ion-suppression and normalizes data.
  9. Mass-spec vendor agnostic; specific extensions for inclusion of Sciex SWATH, and Agilent IM.

Helpful resources

ROUTINELY IDENTIFIED COMPOUNDS IN INTERNAL STANDARD

USER MANUAL

POSTER – Correction of Ion Suppression and Normalization for Improved Quantitative Rigor and Reproducibility using IROA

WHITEPAPER – Integration of Standards for Ion Suppression Correction and QC in an Untargeted Metabolomics Workflow

How to set up and run a C13-labeled Yeast Extract “TruQuant” Calibration Experiment

TruQuant Workflow References:

Charkoftaki, G., Aalizadeh, R., Santos-Neto, A. et al. An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model. Hum Genomics 17, 80 (2023). https://doi.org/10.1186/s40246-023-00521-4

Petrova B, Lacey T E, Culhane A J, Cui J, Raskin A, Mishra A, Lehtinen M K, Kanarek N. Metabolomics of Mouse Embryonic CSF Following Maternal Immune Activation. bioRxiv preprint https://doi.org/10.1101/2023.12.06.570507

Lippa KA, Aristizabal-Henao JJ, Beger RD, Bowden JA, Broeckling C, Beecher C, Clay Davis W, Dunn WB, Flores R, Goodacre R, Gouveia GJ, Harms AC, Hartung T, Jones CM, Lewis MR, Ntai I, Percy AJ, Raftery D, Schock TB, Sun J, Theodoridis G, Tayyari F, Torta F, Ulmer CZ, Wilson I, Ubhi BK. Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC). Metabolomics. 2022 Apr 9;18(4):24. doi: 10.1007/s11306-021-01848-6. PMID: 35397018; PMCID: PMC8994740.

Habet V, Li N, Qi J, et al. Integrated Analysis of Tracheobronchial Fluid from Before and After Cardiopulmonary Bypass Reveals Activation of the Integrated Stress Response and Altered Pulmonary Microvascular Permeability. The Yale Journal of Biology and Medicine. 2023 Mar;96(1):23-42. DOI: 10.59249/kfyz8002. PMID: 37009190; PMCID: PMC10052603.

Piqueras, M.D.C., Myer, C., Junk, A., Bhattacharya, S.K. (2019). Isotopic Ratio Outlier Analysis (IROA) of Aqueous Humor for Metabolites. In: Bhattacharya, S. (eds) Metabolomics. Methods in Molecular Biology, vol 1996. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9488-5_15

Qiu Y, Moir RD, Willis IM, Seethapathy S, Biniakewitz RC, Kurland IJ. Enhanced Isotopic Ratio Outlier Analysis (IROA) Peak Detection and Identification with Ultra-High Resolution GC-Orbitrap/MS: Potential Application for Investigation of Model Organism Metabolomes. Metabolites. 2018 Jan 18;8(1):9. doi: 10.3390/metabo8010009. PMID: 29346327; PMCID: PMC5875999.

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