Prodrome Sciences Inc.

Metabolomics services

Non-targeted, discovery metabolomics for pharma, biotech, food industry, and academia

Prodrome Sciences’ customizable, non-targeted, comprehensive metabolomic platform is now available for contract research services. Our patented complex sample analysis technology was invented in 1999, patented in 2000, and commercialized in 2001. Since 2001, tens of thousands of biospecimens encompassing hundreds of independent experimental designs have been performed. The data generated using the technology has resulted in numerous patents, peer-reviewed publications, and regulatory-approved diagnostics products.


  • Plasma, serum
  • Tissues
  • Cells
  • Organelles
  • Cell culture material
  • Fecal samples
  • Plant material
  • Bacterial and yeast cultures
  • Environmental samples
  • Food samples (food ingredients, functional foods, nutraceuticals, etc.)

A unique service

  • We specialize in non-targeted metabolomics.
  • We help with metabolomics experimental design and work closely with you from inception to the conclusion to help realize your objective.
  • Over 100,000 metabolites have been detected with the technology. Depending on the type of sample being analyzed, a typical project yields over 10,000 detectable metabolites.

4 week turn-around

Results are delivered within 4 weeks from the date we receive your samples (up to 100 samples in 6 analytical modes).

What you get

  • Access to the technology that resulted in ground-breaking discoveries in cancer and neurological diseases.
  • Accurate-mass based, high-resolution mass spectrometry data from 6-modes.
  • Data for about 10,000 metabolites that covers all metabolic systems and provides a complete snapshot of the metabolome.
  • Customized targeted metabolite subsets for accelerated routine analyses and project optimizations.
  • Delivery time: 4 weeks (up to 100 samples in 6 analytical modes).

Ideal for pre-clinical discovery projects (in vitro/in vivo).

Human samples are considered on a case-by-case basis. Due to Prodrome Sciences’ extensive human clinical database (over 8,000 biospecimens and counting), certain conditions apply – contact us for details.

Application examples

  • In vitro studies to identify changes in metabolic pathways due to genetic manipulations.
  • Drug discovery: metabolite identification of candidate molecules and toxicology.
  • Biomarker discovery.
  • Food industry: metabolic changes due to dietary interventions, toxicology, biomarkers, and composition analysis of new dietary ingredients.
  • Cosmetics industry: discovery of new ingredients, toxicology, and new ingredient analysis.
  • Microbiome studies: assaying fecal samples.
  • Studies involving bacterial and yeast genetic manipulations.
  • Plant genetic manipulation of metabolic pathways.
  • Veterinary medicine: diagnostics development, nutritional research, and metabolic disease research. 
  • Academic studies on metabolomics.


Price includes sample preparation, aliquoting, and storage; six independent, high-resolution, accurate-mass analysis modes; and customized data report. Data is also provided in an excel sheet for external statistical analyses.

Clients are responsible for shipping samples to our lab in Carlsbad, CA.

Email us to start your project today or for more information.


$99 / Sample / Mode
  • $10,000 project minimum.
  • 6 independent, high-resolution, accurate-mass analyses each designed to maximally detect a specific metabolome subset (A-ionic bases; B-ionic acids/glucuronides; C-polar bases/neutrals; D-polar acids/neutrals; E-non-polar bases/neutrals; F-non-polar acids/neutrals).


$10,000/ 20 Samples / 6 Modes
$20,000/ 50 Samples / 6 Modes
$35,000/ 100 Samples / 6 Modes
  • For over 100 samples, contact us for a quote.
  • Non-targeted metabolomics is the best available analytical method for hypothesis-generating discovery projects.
  • All 6 analysis modes ensures maximum capture of metabolites.

Prodrome Sciences Inc. reserves the right to refuse service to any individual or entity due to factors within or beyond our control or due to any conflict of interest. The results provided are solely intended for research, non-clinical, and non-diagnostic purposes. Timelines, scope of work, and prices stated here are approximations: the contractual agreement will be final.

“We have used the expertise at Prodrome Sciences Inc. to aid in microbial engineering. The goal was to understand what metabolic changes happen to Saccharomyces cerevisiae when an exogenous aromatic polyketide acid is built intracellularly through genetic engineering. Metabolic engineering is the core of our company; we believe that looking at the complete metabolome is absolutely essential for strain optimization. Prodrome's personalized service, particularly in metabolomic experimental setup and data interpretation, was very helpful and sets them above traditional university and commercial CRO's that we have worked with in the past. The results of the metabolomic analysis gave us an understanding of off target metabolic processes and has led to 4 new genetic designs that would not have been designed otherwise. Prodrome’s customizable non-targeted platform is very useful for discovery projects like ours. We will certainly be using their metabolomic services for our next project."

Dr. Tony Farina CSO, Librede, Inc.

“We used Prodrome’s metabolomic services to investigate changes in the gut microbiome of research animals resulting from drug treatment. Data were very clean, delivered in a timely manner, and with excellent quality control measures. The non-targeted nature of the assay and analysis in different modes were ideal for this kind of experiment, where we look for changes in many different classes of molecules. In addition, they performed targeted, quantitative analysis of specific metabolites. Overall, their quality of service and quick turnaround time was well above industry standards.”

- Dr. Steve Van Dien Co-Founder and CTO, Persephone Biome Inc.


The metabolome

The metabolome is the comprehensive collection of metabolites in the body and is part of the phenotypic expression of genomic, protein, metabolite, and microbial interactions in the body representing the overall functional state at any given time. Comprehensive systematic analysis of the metabolome and any perturbations due to xenobiotics, diseases, or environmental effects is termed metabolomics (PMID: 17134127).


Our technology

Patented technology

Our patented technology (US patent no. US 7349809 B2) is based on flow injection high-resolution, accurate-mass technology which has the ability to identify a larger number of analytes ranging from 150 to 1,000 Da based on accurate-mass (PMID: 12427274), which on principle does not require standards for putative identification. This methodology is best suited for hypothesis-generating discovery projects.

Proven history
Technology advantages
Metabolites detected
Analytical modes

Case studies

Colon cancer metabolomics

Reduced levels of hydroxylated, polyunsaturated ultra-long-chain fatty acids in the serum of colorectal cancer patients: implications for early screening and detection (BMC Medicine 2010, 8:13).

A metabolomic study of serum from three independent populations using FT-ICR technology led to the discovery of novel, 28-36 carbon ultra-long chain fatty acids which were deficient in colorectal cancer (CRC) sera (see the figure below). These molecules differentiated CRC cases from controls with high sensitivity and specificity and commercial screening tests were developed based on this discovery.


Pancreatic cancer metabolomics

Metabolic system alterations in pancreatic cancer patient serum: potential for early detection (BMC Cancer 2013, 13:416).

Several metabolic systems were found to be perturbed in pancreatic cancer compared to the controls when the samples were analyzed by FT-ICR technology. Those metabolic systems were phosphatidyl cholines, lyso phosphatidyl cholines, sphingomyelins (SM), and a certain class of ultra-long chain fatty acids (C28-C36). These discoveries were later used to develop pancreatic cancer screening tests.


Nutraceuticals/functional foods

Murch SJ, Rupasinghe HP, Goodenowe D, Saxena PK. A metabolomic analysis of medicinal diversity in Huang-qin (Scutellaria baicalensis Georgi) genotypes: discovery of novel compounds Plant Cell Rep. 2004 Nov;23(6):419-25.

Metabolic effects of plant genetic manipulation

Zulak KG, Cornish A, Daskalchuk TE, Deyholos MK, Goodenowe DB, Gordon PM, Klassen D, Pelcher LE, Sensen CW, Facchini PJ. Gene transcript and metabolite profiling of elicitor-induced opium poppy cell cultures reveals the coordinate regulation of primary and secondary metabolism. Planta. 2007 Apr;225(5):1085-106.

Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenowe DB, Kitayama M, Noji M, Yamazaki M, Saito K. Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J. 2005 Apr;42(2):218-35.

Aharoni A, Ric de Vos CH, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R, Goodenowe DB. Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS. 2002;6(3):217-34.

Trancriptomics and metabolomics

Yamazaki M, Mochida K, Asano T, Nakabayashi R, Chiba M, Udomson N, Yamazaki Y, Goodenowe DB, Sankawa U, Yoshida T, Toyoda A, Totoki Y, Sakaki Y, Góngora-Castillo E, Buell CR, Sakurai T, Saito K. Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones. Plant Cell Physiol. 2013 May;54(5):686-96.

Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H, Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J, Papenbrock J, Saito K. Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem. 2005 Jul 8;280(27):25590-5

Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10205-10.

Metabolic network reconstruction

Breitling R, Ritchie S, Goodenowe D, Stewart ML, Barrett MP. Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data. Metabolomics. 2006;2(3):155-164.

About Prodrome Sciences Inc.

Prodrome Sciences researches prodromes of diseases – how to detect them, what causes them, and how to return high-risk prodrome states back to a healthy state before the disease develops. We use our advanced diagnostic technology for blood tests to detect disease prodromes and in our natural therapeutic programs to restore an unhealthy, high-risk prodrome state to a healthy, low-risk state. Our goal is to reduce the number of people that develop and die from disease and to promote optimal health.

Keep in touch

©2019 Prodrome Sciences Inc.