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MSF Metabolomics, Lipidomics, and Small Molecules



What types of samples can I send?

  • We accept samples of all types, including tissue, cells, plasma/serum, other bodily fluids (e.g. urine, lavage, etc.), synthetic compounds, environmental samples, and more.
  • Samples we do NOT accept include:
    • Radioactive-labeled samples
    • Samples containing pathogenic or harmful substances that have not been deactivated first using acceptable inactivation protocols**
**Please contact us for acceptable methods to inactivate samples containing pathogenic or harmful substances.

How much sample should I send?

  • The following are the minimum amounts of sample we will need to analyze:
    • Bodily fluids (serum/plasma, urine, etc.): 25 μL
    • Feces: 30 mg
    • Cells: 1-2e6 PBS-washed pellets or 1-2e6 cell suspensions
    • Tissue: 20 mg
    • For other sample types, please contact us directly for more information

  • The above amounts are the minimal recommended sample amounts. However, sending more is always better.
  • When sending samples, be sure to indicate the accurate mass/concentration/volume on your Sample Submission Form. We will need this information when performing data normalization.

How many samples can I send?

  • You may send as few as one to as many as several hundred. However, for optimal results it is best to send samples that are in replicates of 5 and from several different experimental groups (e.g. treated vs. untreated, WT vs KO, etc.), but a minimum of 3 per sample group are needed for any statistical analyses to be done.
  • Additionally, sending blanks, controls, or other standards used in extraction or sample processing will be helpful to eliminate background metabolites during analysis.
  • For untargeted metabolomics we will need at a minimum of 5 replicates from 2 sample groups in order to perform statistical analyses.

How should I send my samples?

  • Frozen samples should be shipped to MSF on dry ice using overnight shipping. We recommend shipping by Tuesday morning to avoid complications with delivery. Please ship to:

UTMB Mass Spectrometry Facility
301 University Blvd., Rm. 2.232 Basic Sciences Bldg., L04569
Galveston, TX 77555-0635

What other information should I send?

  • Please include a Sample Submission Form with your shipped samples.
    • For UTMB on-campus samples, an ISC# must be provided before samples will be processed
    • For off-campus samples, credit card information must be provided to Terry Campbell ( before samples will be processed

  • On the Sample Submission Form, please include the following:
    • What species the samples are from and whether there will be species-specific metabolites to be analyzed (e.g. odd-chain or cyclic lipids from bacteria)
    • Sample names/IDs and sample groups
    • Molecular weights or chemical structures for unusual metabolites to be analyzed

  • A brief description of the project is also welcome as it will help us look into the background literature for a better understanding of how best to analyze your samples. Providing examples from the literature of the type of analysis you desire is greatly appreciated.

How much does it cost to analyze samples?

  • This will depend on how many samples you are submitting, what assay(s) you would like to be done, and how the data are analyzed afterwards. Please contact Prof. Russell ( for a quote on specific costs.


How will my samples be analyzed?

  • Our targeted metabolomics and lipidomics analyses are performed on an Agilent 1260 UHPLC coupled to a SCIEX QTRAP 6500 mass spectrometer. Samples will be extracted by one of the MSF staff members and then processed according to the assay desired. This may include derivatization, solid phase extraction (SPE), or other techniques to optimize analysis.
  • For custom assays or other novel metabolites not part of our established panels, we will optimize ionization and LC gradient conditions using verified standards to develop or add to existing methods.
  • Once samples are injected and the data is acquired, we integrate LC-MS peaks, process data, and perform statistical analyses using a variety of software (Analyst, Multiquant, Skyline, R, Metaboanalyst).

What is the difference between absolute and relative quantitation? Which is best for my samples?

  • Absolute quantitation uses stable isotope labeled homologues of the metabolites to be measured as internal standards.** Usually these standards are spiked into samples prior to extraction. Limits of detection and quantitation (LOD and LOQ) are determined with the linearity of response to determine accurate quantitation of absolute values. This type of quantitation provides quantitative values, such as “nmol/mg”, “μM”, or other units.
  • Relative quantitation uses surrogate internal standards that are chemically similar to a class of compounds but may not be exactly the same. One or a few surrogate internal standards are included to account for many metabolites, and they may or may not be isotopically-labeled. This type of quantitation is useful for determining “up/down” changes between sample types, such as wildtype vs. mutant, or treated vs. control. This type of quantitation may be desired if absolute quantitation is unnecessary to the research goals. Values are represented as “Relative amount” or “Fold difference” or “Peak area ratio” or other arbitrary units.
  • The choice of which quantitation to choose will largely depend on whether absolute, quantitative values are needed or desired, otherwise our analyses will generally default to relative quantitation.
**The use of isotopically-labeled internal standards may increase the cost of analysis depending on the assay requested.

What is the difference between targeted and untargeted analysis? Which is better for my samples?

  • Targeted metabolomics/lipidomics are highly specific for a set of compounds and are accurate for relative or absolute quantitation. Our metabolomic and lipidomic panels are all examples of targeted analyses. This type of analysis is useful for providing answers to biological research questions, such as revealing the physiological state of a sample or exploring the functional impacts of mutant knockouts or drug treatments.
  • Untargeted metabolomics attempts to determine the differences in as many metabolites as detectable between groups of samples. Unlike targeted metabolomics, untargeted analyses are sometimes regarded as “hypothesis-generating” experiments. They are less useful in definitively answering biological research questions as they are useful in providing questions or research directions for future targeted analyses.
  • A major difference between targeted and untargeted metabolomics is that the confidence of correctly identifying metabolites during targeted analysis is much greater due to the combination of tandem mass spectrometry data (i.e. MS/MS) with retention time information that can be related to a verified internal standard. In untargeted metabolomics, compound identity is less certain as it relies on accurate mass searching to compound databases for identification, and rarely contains enough internal standards to account for all possibly identified compounds.

Are you able to do pharmacokinetics-pharmacodynamics (PK/PD) profiling?

  • We can do PK/PD profiling. Contact us to set up a consultation to determine what tissues to analyze, the drug and metabolic intermediates to follow, and what time points to monitor.

Are you able to analyze stable isotopically labeled samples?

  • Yes, we can analyze stable isotopically labeled samples. Let us know what isotopes were used (e.g. 13C, 15N, 2H) during labeling or treatment so that we can adjust our targeted panels to account for the different masses and isotopic incorporation into the metabolites of interest.

What if my metabolites of interest are low abundant?

  • There are a number of strategies we can take to try and analyze low abundant metabolites. This may include derivatization, SPE, or simply concentrating the sample or injecting more extract on to the LC column.

What if my metabolite(s) of interest isn’t part of the assays available?

  • If the metabolite is a close relative to the metabolites in our established panels, it may be a simple matter of adding the precursor and fragment ion masses to those panels and monitoring for your metabolite(s) of interest using the same LC and MS conditions.
  • However, if your metabolite of interest is completely novel, then we can work with you to develop a custom assay to obtain the best LC and MS conditions to monitor for your metabolite(s) of interest.

What if I want to analyze samples with multiple metabolomics/lipidomics panels?

  • Most of our targeted metabolomic and lipidomic panels are compatible with one another so that we can do multiomics, i.e. analyze samples with multiple metabolomic, lipidomic, and/or proteomic analyses. Let us know what panels and analyses you are interested in so that we can adjust our extraction strategy and know what collection of internal standards will be needed.


How will the data be normalized?

  • We can normalize data in a number of ways, including tissue/sample weight, volume, cell number, protein concentration**, or another specified way. Please indicate how you would like to normalize your data on the Sample Submission Form when you send your samples, and please indicate the amount if you are providing these normalizing values with as much accuracy as possible.
**Protein concentration can be determined by MSF as part of the extraction procedure for an added fee per sample.

How will the data be returned?

  • Generally, we provide a PowerPoint document that gives an abbreviated overview of the methods used and the key findings of the analysis, which may include bar charts, scatter plots, heatmaps, or other statistical tests and figures. We also provide an Excel document that contains all the processed data and the LC-MS peak integration values before processing. Processing of the data will usually involve normalization, averaging and standard deviations of replicates within sample groups, and statistical analyses where appropriate.

Is the raw data available? Will it be uploaded to a publicly available database?

  • We can provide the raw data files upon request. However, we cannot provide the software** used to analyze the data due to licensing restrictions on commercial software or other open-source software that we use is already available elsewhere.
  • We do not upload raw data to public databases unless requested.
**We can provide guidance and support if you decide to analyze raw data yourself using your own copy(ies) of data analysis software. See following question.

Can I analyze the raw data myself?

  • We do have a “How-to” tutorial on LC-MS peak integration using Skyline software (freely-available and open-source) if you would like to analyze raw data yourself. Contact us for more information if you are interested.

How long will it take for samples to be analyzed?

  • This is highly dependent on the number of samples submitted, how many samples from other labs are currently being analyzed in the core facility or waiting to be analyzed, whether method development is required, and the complexity of the analysis involved. However, in general we can analyze samples and return data within 2-3 weeks of receiving samples.

What if my data doesn’t look right?

  • Contact us immediately if you believe there are discrepancies in your data. We hold on to sample extracts in -80°C freezer storage if they require re-analysis, and we can always reanalyze already acquired data if there are issues there.


Do I need to list an MSF member as a coauthor?

  • While this is not a requirement, if you believe a staff member of MSF provided in-depth analysis, experimental design, or otherwise contributed to the intellectual merits of the project, then we would greatly appreciate being included as a coauthor.

How should I describe the methods under “Materials and Methods” sections of a paper?

  • The reports we provide following an analysis will have an abbreviated description of the methods used to analyze your samples. If you require a more detailed description, we can provide this as needed.

Do I need to acknowledge MSF?

  • YES, please acknowledge MSF within the acknowledgments section of any papers that use data produced by MSF.
  • MSF is also supported in part by Cancer Prevention Research Institute of Texas (CPRIT) grant number RP190682. Please acknowledge this funding in your publication.