Mass Spectrometry & Proteomics Core Facility

A Newsletter from MSPCF 

Welcome to our very first newsletter issue! We want to keep you informed on what everything new and interesting is going on in our Core and in the field of mass spectrometry. We will be sharing these updates now quarterly. At the University of Nebraska Medical Center, we are very proud to support the research community and be witnesses of great ideas and new discoveries! 

We have lots of exciting news to share in this issue: 

 New space
                      New equipment
                                           New people! 

As the pandemic is still around us, and I am sure we all got some COVID-19 fatigue, we cannot yet provide in-person trainings for our students and research staff, however we will be working diligently to bring our trainings online! Our YouTube channel is planned to be open by the end of the year. Until then, we are always available to answer all of your questions regarding mass spectrometry.


Dr. Dragana Lagundžin
MSPCF Manager


Let's start with NEW PEOPLE
Rafay and Dhananjay joined our team this year!

My Short Mesmerizing Story (MS/MS)

It was freezing cold when I first came to UNMC and joined the core in the month of January, 2020. Being from the southern part of India where climate is mostly tropical, the nail-biting snow-white weather of Omaha appeared to be frightening at first. But the moment I met the members at the core, their warmth and welcoming happy faces melted away all my frozen worries instantly. This, my team, is the best part about working here at the MSPCF core.

Apart from enjoying the company of my teammates, I spent most of my time interacting with my favorite MS system, Thermo Orbitrap Fusion Lumos. The exceptional capabilities and state-of-art orbitrap technology in this system provide plethora of opportunities to carry out meaningful scientific discoveries. For the last two decades, advancement in orbitrap technology has contributed significantly in the field of proteomics and metabolomics. Incidentally, I was always fascinated by proteins, their marvelous intricate structure and associated functions. The apparent impact of mass spectrometry-based proteomics in exploring the mysteries of biological functions of proteins attracted my interest into this field. My efforts in future will be focused in creating novel strategies using MS as a tool to make progress in our understanding towards molecular function of proteins implicated in physiological conditions and development of bio-pharmaceuticals.

- Rafay Abu, MS
   Mass Spectrometry Specialist

Meet Dr. Dhananjay Shinde! 

What is so special about working in the Mass Spectrometry Core?
- I always wanted to pursue analytical chemistry that makes me able to see the molecular processes using modern analytical technique such as chromatography-mass spectrometry. MS core is a centralized technology-based laboratory which maintains and support sophisticated mass spectrometry instruments for use by UNMC’s researchers from across the discipline. Working in MS core brings you to face new problems which initially are frustrated but are rewarding.

What is your favorite mass spec? 
- Newly installed Sciex hybrid triple quadrupole- ion trap connected with the Waters ultra-performance liquid chromatography (UPLC) is one of my favorite mass spectrometer in the core. This MS is very sensitive and provides absolute and relative metabolites quantitation in a variety of biological and chemical matrices.
Favorite field in mass spectrometry?
- My favorite field of research is metabolomics, lipidomics and heavy labeled-flux analysis. These fields represent the complete set of metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes. Thus mass spectrometry provides quantitative readouts of the physiological functions and provide information for the better understanding and interpretation of cellular biology.
Future goals?
- My future goal is to study and establish the links between metabolomics and lipidomics in cellular functions.

- Dhananjay Shinde, PhD
   Senior Scientist

We've got new EQUIPMENT on board
Newly installed hybrid Triple quadrupole-ion trap mass spectrometer (QTRAP 6500+) from Sciex is highly sensitive MS that provides best limits of quantitation over the widest range of compounds. Highest scan speed of the mass spectrometer at 20000 Da/sec enhances our capabilities of detecting and identifying compounds across a wide scope of chemistries with low mass or high mass, positive or negative polarity at once. IonDrive technology built into the system, from the ionization source, through the ion-focusing region gives us the lowest LLOQ for compounds of many classes, even in complex matrices, for robust and reliable results without substantial interference of matrix. QTRAP 6500+ MS coupled with the highly efficient and robust ultra-performance liquid chromatography (UPLC) Acquity I class from Waters, provides maximized peak capacity, high throughput, and better sensitivity.

Our TripleTOF™ 6600 from Sciex just got the new Optiflow interface! With the new interface, we can now easily change flows between nano and micro, and accomodate new projects, TripleTOF integrates qualitative exploration, rapid profiling, and high-resolution quantitation workflows on a single platform. It contains the high sensitivity detection and high-resolution with at least 5X better acquisition speed. Using SWATH™ Acquisition technology, simultaneous quantitative and qualitative detection is possible of all proteins and peptides in a single analysis.

MSPCF has more SPACE 
We are still located at DRC I, 1st floor, but our Core now has additional space for our equipment, sample preps and trainings. 
Room 1050: This is our space for Orbitrap Fusion Lumos and MALDI-TOF/TOF. Additionally, we have a new set up for offline HPLC fractionation: Vanquish UHPLC (Thermo) and Acquity  UPLC H class (Waters) systems. Inside of the room 1050, there is additional room 1050B, where we have our QTRAP 6500+.
Room 1058: This is our space now solely for our TTOF 6600
Room 1027: Our lab is located here, ready for all sample preparations and trainings. 
Room 1045: This is our data analysis room available for all users. We have separate stations for different search platforms. You can reserve your time on RSS.
Researchers In The MSPCF Spotlight
Early Career Leaders

Meet Dr. Lie Gao
About me: Lie Gao is Assistant Professor at the Department of cellular & integrative physiology, College of medicine, UNMC.

My research: The nuclear factor (erythroid-derived 2)-like 2 (Nrf2)/Kelch ECH-associating protein 1 (Keap1) complex is a master transcriptional regulatory system responsible for cytoprotection against multiple stress challenges. Under basal conditions, Nrf2 is sequestered in the cytoplasm by its tether, Keap1 and rapidly degraded via the Cullin 3 ubiquitin-proteasomal system. When reactive oxygen species or other stressors are increased, Nrf2 liberates from Keap1 and translocates to the nucleus where Nrf2 binds to antioxidant response elements (AREs), leading to coordinated activation of a broad array of genes encoding proteins involved in anti-oxidation, anti-inflammation, detoxification, and metabolism. To determine the functional significance of Nrf2 in skeletal muscle, we created two tissue-specific transgenic mouse models, iMS-Nrf2flow/flox and iMS-Keap1flox/flox mice. These two models allow us to delete or overexpress (i.e. Keap1 KO) muscle Nrf2 that is, in turn, expected to correspondingly change the broad downstream target proteins and molecular networks.

How Mass Spec Core helped my research: Current research in the Nrf2 field is limited because it has largely been driven by candidate gene/protein approaches, such as polymerase chain reaction and immunoblotting, where the specific targets are selected in advance for study based on their known roles. In contrast, the MSPCF Core provides an unbiased discovery-based approach, proteomics, which allows us to explore the functions of the Nrf2/Keap1 system by uncovering unknown Nrf2 target proteins and downstream pathways to the fullest. Indeed, by utilizing mass spectrometry analysis of Nrf2- and Keap1- null skeletal muscle, we identified more than 200 differentially expressed proteins that enable us to propose a novel “two-way model” to understand Nrf2 functional significance in skeletal muscle. This study is currently in press in the Journal of Physiology and available online in

Meet Dr. Henry C.H. Law
About me: My name is Henry and I am a postdoc working in the Eppley Institute, at the UNMC. I am born and raised in Hong Kong.  I got my Ph. D. degree from the University of Hong Kong in 2016. My Ph. D. thesis focuses on developing novel chromatography techniques for proteomics analysis. My expertise in proteomics leads me to UNMC in 2017. Since then I have been working for Dr. Nicholas Woods and engage in cancer research.

My research: Using the instrumentation in the Mass Spec Core, I have established the first proteomics-based pancreatic ductal adenocarcinoma classification system. It separates the tumor and the associated tumor microenvironment into 4 subtypes: metabolic, progenitor-like, proliferative and inflammatory. The subtypes showed association with the patients' drinking and smoking history, as well as the potential benefits to chemotherapy. With further validation, the PDAC subtype can be used as a prognostic marker in a clinical setting. This study is published in the Clinical Cancer Research:

How Mass Spec Core helped my research: The proteomics data were acquired with the Orbitrap Lumos in the Core. The MS3 TMT workflow I used improves the accuracy of TMT quantitation by removing the isobaric contaminant in the background, leading to more reliable results. Since the last project, I have been using the services provided by the MSPCF. They have been providing expert opinion in experimental designs and grant applications. I really like their fast turnaround time and I am looking forward to working with them in my upcoming projects.

Why should we care about proteins and PROTEOMICS
Watch the video below from Heck Lab (Utrecht University, Netherlands) about the
Fascinating World of Proteomics 

Tip Of The Month

Make Reviewer #2 Happy: Plan at least 3 replicates for your MS experiment :) 

University of Nebraska Medical Center