CBMSR mass spectrometry exampleApplications

Mass spectrometry is an analytical technique that measures the mass of atoms and molecules to determine the chemical composition of analytes in a sample.

Broadly speaking, mass spectrometry can be used to measure virtually any chemical or biological molecule. Applications in biomedical research include identification, characterization, and quantification of peptides, proteins, glycans, lipids, metabolites, drugs and other small molecules.

With technologies we have available in the Center, we have the flexibility to identify analytes without knowing their identity a priori, or we can achieve robust quantitative measurements for pre-defined molecules of interest. We can also perform qualitative characterizations, such as the structure of a small molecule or post-translational modifications on a protein, among many other applications.

Learn more about the most popular applications listed below. Some applications are ready for fee-for-service, while others require extensively tailored methods best suited to collaborative agreements.

Mass spectrometry technologies and approaches are rapidly evolving, so if you don't see your desired application listed here, please don't let that stop you from contacting us – we are eager to incorporate new methods into our workflows to meet the needs of Investigators.

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  Qualitative Proteomics

There are a virtually unlimited combination of modern proteomic and mass spectrometry approaches that can be combined to identify and characterize proteins. Our technologies support both peptide-level (e.g. bottom-up) and protein-level (e.g. top-down) analyses. These applications can be applied in "discovery mode", where the protein of interest is not necessarily known a priori, or in "targeted mode", where the sequence and modifications of a particular protein of interest are interrogated.

Types of qualitative experiments we support in the Center:

Identification of peptides and proteins from biological samples
This includes, but is not limited to proteins provided in the form of 1-D gel bands, purified proteins, whole cell or tissue lysate, and biological fluids (e.g. serum, plasma, vitreous fluid, cerebral spinal fluid, etc.).

Identification and localization of post-translational modifications
This includes, but is not limited to phosphorylation, ubiquitination, sumoylation, acetylation, glycosylation, and oxidative modifications. Depending on the goal of the study and modification type, specialized preparation workflows may be used to enrich for proteins or peptides with the modification of interest.

Top-Down proteomics to map protein proteoforms
In "top down" analyses, intact full proteins are analyzed directly in the MS to detect degradation products, sequence variants, and combinations of post-translational modifications. This analysis is done on an entire protein molecule without enzymatic digestion, thereby maintaining relationships of modifications throughout the length of the protein. This can be done on purified proteins, simple, and complex mixtures.

  Quantitative Proteomics

Mass spectrometry is not inherently quantitative because of differences in the ionization efficiency and/or "detectability" of the many peptides in a given sample. Consequently, this has fueled the development of elegant experimental methods to determine relative and absolute abundance of proteins in samples. While the intensity of a peak in a mass spectrum is not a good indicator of the amount of the analyte in the sample, differences in peak intensity of the same analyte among multiple samples accurately reflect relative differences in its abundance.

Types of quantitative experiments we support in the Center:

  • Label-free quantitation by data dependent acquisition (DDA) based on precursor ion intensity.
  • Label-free quantitation by data independent acquisition (DIA).
  • Isobaric Tags (e.g. TMT)
  • Metabolic Tags (e.g. SILAC)
  • Targeted quantitation (e.g. PRM, SRM)

Learn more about quantitative approaches.

  Structural Proteomics

To understand a biological system, knowing protein identity, modifications, and relative abundance are often just the beginning. Augmenting this information with an assessment of protein structure and interaction partners can provide the keys to understanding protein function.

Types of structural proteomics experiments we support in the Center:

Identification of disulfide bonds in intact proteins or between peptides
Using a combination of fragmentation techniques, we are able to map which cysteines in a protein share a disulfide bond.

Identification of binding partners
Combining state-of-the-art sample preparation workflows, quantitative mass spectrometry, and advanced bioinformatics for "interactome" studies, we can identify proteins that interact with target proteins of interest. We suggest tandem affinity tags (TAP-tags) and enzyme-catalyzed "proximity labeling" approaches such as BioID, APEX, and others, when possible.

Hydrogen/Deuterium Exchange
HDX is a powerful approach for assessing 3D structure, protein-ligand, and protein-protein interactions. We plan to offer HDX workflows starting in 2018.

  Chemical Proteomics

Chemical proteomics approaches can be used in many aspects of small molecule drug research, including identification of drug targets, quantitation of drug-protein interaction affinity, profiling enzyme activity, and selectively profiling proteins with specific characteristics.

Details regarding the types of chemical proteomics approaches we support in the Center will be included as they become available.

  mAb Characterization

We offer several strategies to characterize mAb:

Sequencing from the bottom-up
Using high mass accuracy peptide-level information and advanced bioinformatics in Supernovo, we can assemble peptide sequences onto a mAb framework and provide quantitation of variant relative to the unmodified sequence.

Profiling from the top-down
Using powerful top-down proteomics approaches coupled with Orbitrap technology, we can provide mass differences on an intact antibody (and to count the number of modifications).

For antibodies that target extracellular domains of cell surface proteins, we can help you validate the antigen using the Ligand Receptor Capture Technology. In this approach, we can help you validate that antibodies are specifically recognizing an antigen of interest, can help you identify the receptor for antibodies whose target is unknown, and can help identify putative binding partners for antigens of interest.

  Targeted Metabolomics

We are actively working to implement modern strategies to perform multiplexed quantitation of primary metabolites related to glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, amino acids, and nucleotides. We expect to have these available as fee-for-service work beginning in late 2017.

If you are interested in these types of assays, please let us know and we will work to implement strategies that can benefit your research.


We are actively working to implement state-of-the-art approaches for the analysis of glycans, glycopeptides, and glycoproteins.

If you are interested in these types of assays, please let us know and we will work to implement strategies that can benefit your research.