Proteomics 102: Data Acquisition

Date/Time: April 27, 2023, 10-11 am

Location: NMS 1.120

This class is part 2 of our 3-part series of interactive classes on proteomics, from experimental design to data analysis. Proteomics 102 will be of use for folks considering doing a proteomics experiment, seeking advice before preparing for their next experiment, or who want to understand better how LC-MS/MS data is acquired. The cost will be $46/session.

Thermo Fisher Lunch and Learn Seminar

Date/Time: March 9th, Thursday, 12 pm-1:30 pm (lunch provided)

Location: NMS 1.120

Registration link:

Scale up your biological research: Delivering comprehensive LC-MS workflows to expand your experimental capabilities. Learn about the advantages of doing proteomics on the new Thermo Orbitrap Ascend mass spectrometer.

Speaker: Scott Peterman, Ph.D., Thermo Fisher Life Science Mass Spectrometry Group

Proteomics 101: Experimental Design and Sample Preparation

Date/Time: February 16, 2023, 10-11 am

Location: NMS 1.120

We are starting a 3-part series of interactive classes on proteomics, from experimental design to data analysis. The first part will be held on February 16 and will be of use for folks considering doing a proteomics experiment, seeking advice before preparing for their next experiment, or who didn’t get the results they expected last time. The cost will be $46/session. To register, email with your name, PI, and account number.

Imaris 9.9 Software Is Now Available

The CBRS Microscopy and Imaging Facility is excited to offer our users the latest version of the Imaris image analysis software. The analysis workstation in MBB 1.426S has been updated to Imaris 9.9 for Cell Biologists plus Filament Tracer, and we’ve installed a new Imaris 9.9 Essentials license on our workstation in HDB 3.222K.

Software capabilities include: 3D/4D rendering and movie making; segmentation and measurement; colocalization; object tracking; filament tracing and measurement; and integration with other software, including Matlab and LabKit for machine learning.

Imaris available to our users at no cost, and if you’re interested, please email

Holiday Break

We will be closed for the holiday break from Dec. 24 through Jan. 2. The final day to submit for protein digest is Tuesday, Dec. 22 at noon. The final day to submit ready to run samples is Dec. 23. Samples submitted during the week of Dec. 21 will run over the break and the data will be analyzed in January.

New Staff Member

We are delighted to announce that Peter A. Faull, Ph.D. has joined the facility as Principal Proteomics Scientist. Read more about his scientific journey here.

Proteomics Research & Course Updates

Please join us for a weekly online series of proteomics presentations/journal club to hear about recent proteomics research at the facility or around Texas and learn more about new techniques. Contact to get the Zoom link.

We are taking a break from proteomics to talk about pandemic! We will have an informal group discussion of COVID-19 disease with Dean Brent Iverson giving an insider view on May 7 at 4 pm. Learn more about coronavirus and COVID-19 from Nature and Science. The following week will be Dr. Elyssia Gallagher from Baylor University speaking on “Pushing the boundaries of H/D exchange-mass spectrometry to analyze glycans” on May 14 at 3:30 pm.

CH N190/N153K, Mass Spectrometry for Chemists, will be taught this summer by Dr. Ian Riddington, Director of the Chemistry Mass Spectrometry Facility.

Course Description: Mass Spectrometry is an incredibly powerful analytical technique. It has a multitude of applications from measuring contaminants in drinking water, to detecting post translational modifications in proteins. Being such a huge field though, it can be overwhelming, especially as many students have never taken a mass spec class.

This course is aimed at the Chemist/Biologist/Engineer that is using Mass Spectrometry in the course of their research. The overall aim is to bring together many seemingly unrelated areas of chemistry, in a way that will enhance understanding. That in turn will allow students to obtain maximum benefits from the instrumentation available at UT Austin.

Colony Management: Genotyping Assistance During and After the COVID-19 Crisis

To help researchers manage their mouse and rat colonies, the MGEF oversees the Transnetyx TAGCenter kiosk located in the ARC Annex near the second-floor break area. Transnetyx offers automated genotyping with a reported accuracy of 99.97% and results in 24 or 72 hours. Free supplies are located at the TAGCenter.

To use the TAGCenter:

  • Collect your tail snips or ear punches in the 96-well plate
  • Scan your MyTAG badge and your well plate’s barcode at the TAGCenter
  • Deposit your well plate in the kiosk pass-through slot
  • View the drop-off time and the results time
  • Receive an email from Transnetyx when your printable, exportable samples results are available in your secure, online account

The MGEF ships the deposited well plates on Tuesdays and Thursdays after 3 pm.

Restart Planning: Rapid Expansion of Transgenic Lines by IVF Speed Expansion

To avoid lengthy delays in expanding mouse colonies by traditional breeding, the MGEF can perform IVF to generate large numbers of cohort mice rapidly. The advantages of IVF are:

  • Requires only two breeder males or previously cryopreserved sperm
  • Produces a large number of same-age mice
  • Uses oocyte donors from commercial vendors
  • Saves months in breeding time

Contact Bill Shawlot for more information.

Proteomics Facility

The Proteomics Facility will continue accepting and processing samples but the lab will remain locked.

MBB 1.420 lab access requires advance notification and scheduling, contact the lab at 512-471-2895 or, this requirement includes dropping off samples or use of equipment and computers.

Wear gloves before entering the lab, sign in and sign out is required.

Consultations will be held by phone or teleconference.

In-service Day

Most CBRS cores and facilities will have a in-service day today to get processes in line with the VPR’s guidance for research operations at UT. We hope to be operating within the new parameters tomorrow Tuesday March 17. The STEM store is open today 9am to 1pm. The BioResCo and Electronics Services are operating.


The new MALDI is available for self-service usage after training. It has been used locally to detect peptides, proteins, oligonucleotides, chemicals and polymers. Contact Ian Riddington at for training on chemicals or polymers, and contact Michelle Gadush at for training for peptides and proteins.


The QExactive is now available for untargeted metabolomics experiments with data analysis using Compound Discoverer.

Name Change

Our name is changing from Proteomics to Biological Mass Spectrometry Facility as we have now added metabolomics services and instrumentation to the facility.

Grant Application Assistance

For professors without any active grant funding, we have a pilot program to support their obtaining new data for grant applications. They can apply for funds to be spent at the Proteomics Facility. Please contact Maria Person at for more information. Note that if the professor has grant funding for any project, proteomics related or not, they will not qualify for this program.

Mouse Genetic Engineering Facility Releases New Publication

Dr. William Shawlot, Director of the Mouse Genetic Engineering Facility, is co-corresponding author with Som Mukhopadhyay (College of Pharmacy) on Taylor, C. A., Shawlot, W., Ren, J. X., & Mukhopadhyay, S. (2019). Generation and validation of tissue-specific knockout strains for toxicology research. Current Protocols in Toxicology81, e86. doi: 10.1002/cptx.86

Click this link to read paper.

Mass Spectrometry Imaging Core Awarded CPRIT Grant

A CPRIT grant has been awarded to build a High Performance Mass Spectrometry Imaging Core Facility that will develop novel methods to provide detailed molecular information for tissue imaging. State of the art mass spectrometry equipment will be purchased to utilize both MALDI and DESI ionization sources with ultra-violet photodissociation MS/MS fragmentation for cancer research. Jennifer Brodbelt is the P.I., working in partnership with Livia Eberlin and Maria Person. The facility is expected to begin operations in the spring of 2020.

New Installation of Bruker Autoflex and Thermo QExactive

The Biological Mass Spectrometry core is installing a new Bruker Autoflex and will soon have MALDI-TOF/TOF available for self service for checking molecular weights, doing polymer analysis, TLC plate reading, and MS/MS for structural characterization

The new Thermo QExactive installation is in process and will be set up to conduct untargeted metabolomics experiments by late fall.

Fall 2019 Short Courses

Fall 2019 Short Courses are now open for registration! Training in computational and bioinformatics approaches to biological problems is an important part of the CBRS mission. To learn more and register, please visit this link.

CBRS Newsletter

The CBRS newsletter is available here. Read on to see what our core facilities, which provide access to cutting-edge technology and expert advice to enhance your research.