Mass Spectrometry & Proteomics Core Facility


Ms. Spec guiding you through proteomics world 

- Sharing knowledge is caring -

To help our students, and basically everyone who planned on doing some new nice proteomics experiments this year, and cannot get trained by our MSPCF Core members due to ongoing pandemic, Dr. Dragana Noe stepped forward with the YouTube channel Ms. Spec!
You can follow Ms. Spec as she will be posting informative videos and step-by-step tutorials of different mass spectrometry protocols, data analysis, tips and more. Ms. Spec channel will be shared on our MSPCF website!

Click on the video below if you are interested in doing gel-based proteomics. Ms. Spec was using some beer samples for this experiment, so 'To beer, or not to beer?'


Members of Our Team
Meet Eric Troudt!

If you ever used our Core services, you probably had a pleasure to meet Eric!
You also probably know that Eric is almost always available to take over your samples for mass spec analysis at DRC1 room 1050, but here are the things that you might not know about Eric.

'Probably the biggest reward for me is just being able to contribute to a wide variety of projects that are advancing the knowledge and understanding of many diverse areas in biomedical research', says Eric. He believes the field of proteomics represents a vital avenue for gaining new insights into the molecular mechanisms of various human diseases and disorders, and gives a great meaning and purpose!

While the workflows of proteomics experiments can be technically demanding and difficult to master, Eric thinks the biggest challenge for him has been learning the fundamental importance of solid communication with users prior to sample submission, which will help to prevent unnecessary setbacks or shortfalls later on. The establishment of a strong two-way dialogue will allow for many crucial areas of a proteomics experiment to be discussed and reviewed, including:

Determination of project goals

Development of appropriate experimental designs

Proper understanding of both the capabilities and limitations of mass spectrometry for proteomics

Identification of any pre-existing issues or incompatibilities with samples that need to be addressed before submission

Researchers In The MSPCF Spotlight
Early Career Leaders

Meet Dr. Tammy Kielian

About me: I am a Professor in the Department of Pathology at UNMC and hold the Choudari Kommineni, DVM, PhD Endowed Professorship in Pathology. I have been at UNMC since 2008 and have a wonderful group of researchers in my laboratory as well as fantastic collaborators across the UNMC campus.

Our research: My laboratory studies the innate immune response to Staphylococcus aureus (S. aureus) biofilm. Biofilms are complex communities of bacteria where a subpopulation of organisms are metabolically dormant, which is one attribute responsible for their tolerance to antibiotic therapy. S. aureus is a leading cause of biofilm infections associated with prosthetic joints and complications following a craniotomy, a neurosurgical procedure to access the brain for resection of tumors or epileptic foci. Our laboratory was the first to propose that S. aureus biofilms actively elicit an anti-inflammatory immune signature to explain, in part, why biofilm infections are difficult to eradicate in an immune competent host. This is achieved by the preferential recruitment of myeloid-derived suppressor cells (MDSCs) in addition to polarizing monocyte/macrophage infiltrates towards an anti-inflammatory phenotype. We utilize mouse models of S. aureus prosthetic joint and craniotomy infection to study S. aureus biofilm-immune crosstalk, with the ultimate goal of identifying ways to augment host pro-inflammatory responses to promote biofilm clearance. Emerging areas of interest include immunometabolism and how S. aureus biofilm-leukocyte metabolic crosstalk influences the epigenetic landscape of leukocytes to promote their anti-inflammatory attributes.

How the Mass Spec Core Helped Our Research: We recently utilized the Mass Spec Core to characterize the proteome of a S. aureus mutant (ΔatpA) with impaired oxidative metabolism. The rationale for this approach was that S. aureus ΔatpA biofilm transformed the typically anti-inflammatory bias of immune cells to a pro-inflammatory state and we were interested in identifying potential biofilm-derived factors responsible for this process. LC-MS/MS found that numerous bacterial toxins and proteases were significantly reduced in S. aureus ΔatpA biofilm. Therefore, the enhanced pro-inflammatory response in response to S. aureus ΔatpA biofilm was attributed, in part, to increased leukocyte survival. This study was recently published in mBio ( and revealed a critical role for S. aureus ATP synthase, and bacterial metabolism, in shaping the host immune response to S. aureus biofilm.

Meet Dr. Samantha Swenson

About me: I am a Postdoctoral Fellow in the Department of Genetics, Cell Biology, and Anatomy, College of Medicine, UNMC. My PhD is in Biochemistry from UNL and my dissertation was focused on the Heme A Synthase protein Cox15 and how mutations to this protein alter Complex IV assembly via loss of Heme a resulting in Cox1 destabilization. I was recruited by Dr. Shannon Buckley for my biochemistry expertise and I have been working in her lab since late 2017. 

My Research: Our lab is examining the role of the ubiquitin proteasome system in regulating cell fate decisions in normal and malignant hematopoiesis. We are employing both proteomic and genetic approaches to identify potential substrates of E3 ligases implicated in leukemia and lymphoma development and using those substrates to develop novel drug therapies for patients. The E3 ligase that I primarily study is the ubiquitin protein ligase E3 component n-recognin 5 (UBR5). UBR5 is a HECT E3 ligase that plays a role in many pathways in the cell including metabolism, apoptosis, angiogenesis, gene expression, and genome integrity. Overexpression of UBR5 has been found in several solid tumor cancers and monoallelic mutations in UBR5 have been found in ∼18% of patients with mantle cell lymphoma - a rare, aggressive form of non-Hodgkin lymphoma with only a 50% 5-year survival rate. To understand how these UBR5 mutations in MCL are contributing to disease development and progression, our lab has generated a mouse model that mimics these patient mutations, and we are using it to study B cell development in the presence and absence of UBR5 mutations.

How the Mass Spec Core Helped My research: Historically, cancer research has relied on gene expression profiles to identify potential therapies; however, we have found that by using this method, a whole scope of dysregulated proteins are being missed. As such, we are using the mass spec core for our analyses to help us to identify proteins that are differentially expressed to develop therapeutic treatments. We use a TMT method of labeling our mouse samples so that we can have a direct comparison of protein abundance between wild-type and mutant mice. These labeled samples are then analyzed by the core using their Orbitrap Lumos machine. By using Mass Spectrometry analysis, we were able to identify a novel involvement of UBR5 in the stabilization of several components of the spliceosome. This study is published in the American Society of Hematology journal Blood available online at . We have also utilized the mass spec core for several of our other studies including one published in the journal Cancers available online at as well as two that are currently in preparation. We greatly appreciate the Core’s rapid turnaround time and technical expertise when troubleshooting our experiments and performing data analysis. 


We got our results back, now WHAT???

We know that showing your mass spectrometry results can be tricky, especially if you ended up with THOUSANDS of proteins to care about.
Rest assured, that we can help you with this step too, so that your figures for manuscripts, grants, posters, lab meetings, or just to impress your friend (me, being shameless) can look awesome!
Or, if you think you know your goals and results better than us, but need that not-so-cheap program to process your data and make it beautiful, we are here to help, too!

Tip Of The Month

Stay healthy and happy in 2021, and everything else will fall into place, including those MS/MS peaks that are sometimes hard to catch!

University of Nebraska Medical Center