Facility Pictures


Goal of the Facility

The goal of the Mass Spectrometry Imaging Facility is to provide high-quality, spatially resolved, biomolecular information from tissue sections to support cancer research applications.  Mass Spectrometry Imaging (MSI) is performed using Matrix Assisted Laser Desorption/Ionization (MALDI) on three different complementary mass spectrometry platforms.  The variety of instrumentation allows for a wide range of biomolecules to be detected in situ from tissue sections including proteins, peptides, lipids, and metabolites.  The Facility is supported by a Cancer Prevention and Research Institute of Texas (CPRIT) grant.


What is MSI?

MSI is performed by first collecting thin tissue sections, similar to those used for histological analysis, onto a slide that is compatible with the mass spectrometer.  The section may be subjected to one or more aspects of sample preparation including tissue washing or fixation, on-tissue enzymatic digestion or derivatization, and finally matrix application.  Spectra are then collected from the tissue section in an ordered array with a fixed distance (pixel size) between acquired spectra.  Spectra are compiled into a single image file and an average spectrum is used for navigating the data.  Each peak from the average spectrum can be displayed as a function of its spatial localization and relative intensity across the tissue section.


MALDI Imaging

While a several different ionization sources can be used in MSI experiments, the MSI facility at UT Austin is focused on MALDI for ion generation.  MALDI Imaging requires the addition of a chemical matrix to the surface of the section.  The matrix is typically a small aromatic molecule that can ionize biomolecules in the tissue by acting as either a proton donor or a proton acceptor.  A pulsed laser is fired at the surface of the tissue which helps to desorb molecules from the surface and facilitate the ionization process.  Ionized molecules can then be detected within the mass spectrometer.  Spectra are collected at regular distances by moving the sample stage relative to the fixed laser position.  The distance moved between spectral collection corresponds to the pixel size within the image.  Commercial instruments are capable of image resolutions of ~10 µm, although this spatial resolution comes at the expense of sensitivity and is not necessary for all experiments.  The facility has both vacuum and atmospheric pressure MALDI capabilities, broadening the range of types of samples that can be analyzed, inlcuding those that are not vacuum stable.


Histology-Guided Mass Spectrometry Profiling

Histology-Guided Mass Spectrometry (HGMS) Profiling is a specialized type of mass spectrometry imaging.  In this approach a stained serial section of the tissue specimen is used to guide the data collection from specific locations within a tissue section.  A pathologist or clinician reviews a digital image of the stained section and places small, color-coded, circular annotations at the desired locations for data collection; with about 20 annotations per histology of interest per tissue.  These annotations are typically 50-200 µm in diameter and correspond to the size of the area sampled on the tissue.  The annotated image is digitally merged with an image of a serial unstained section and data collected from just the locations of the annotations.  Each spectrum is, therefore, enriched for a single cell type allowing a molecular profile for that cell type to be generated.  The HGMS approach is higher throughput than standard MSI and allows for more facile statistical analysis of the collected data.


Biofluid/Cytology Profiling

Biofluid/Cytology Profiling is also a useful technique for the study of diseases from samples collected in a less invasive manner than a traditional biopsy.  Mass spectrometry profiling technology can be applied to cytology specimens such as fine needle aspirates or scrapes/smears of cells.  Additionally, biofluid profiling without fractionation can be used for the study of disease, although this approach has proven much more successful when the fluid is directly related to the disease being studied (e.g. urine for bladder cancer, cerebrospinal fluid for neurological disorders).  Serum suffers from dynamic range issues rendering relevant biomolecules often too dilute for detection without fractionation or enrichment.


Ultraviolet Photodissociation (UVPD)

Ultraviolet Photodissociation uses laser pulses at UV wavelengths to fragment molecules for identification.  UVPD has advantages over other fragmentation techniques in that posttranslational modifications are often kept intact allowing for their confident localization within a peptide or protein.  It also generates distinct fragments from lipids that allow for positional localization of double bonds in fatty acids.


Data and Statistical Analysis

Mass Spectrometry Imaging data are far too complex to achieve a thorough understanding through manual examination alone.  Statistical analysis tools are employed to determine biomolecules that show positive or negative correlations within tissue images.  Unsupervised segmentation is performed to determine areas of similarity and difference based on molecular signatures.  For larger clinical studies, hypothesis testing, discriminant analysis, and machine learning algorithms are employed for biomarker discovery as well as diagnostic and prognostic purposes.



When using core services, please remember to cite the Mass Spectrometry Imaging Facility in your publications, and funding source CPRIT RP190617 when work was billed at the subsidized CPRIT rate, and send the citation to Erin Seeley. Continued support for the facility depends on documented outcomes.