Identification of protein bands from Coomassie and mass spectrometry-compatible silver-stained gels: This includes reduction/alklylation of cysteines, in-gel digestion with trypsin, followed by a standard 90 minute nano-RP-LC-MS/MS data acquisition, database search using either X!Tandem/TPP or Proteome Discoverer 2.1 (SEQUEST) and delivery of results (either as an e-mail link or an excel file format).
Shot-gun proteomic analysis of complex mixtures by tandem mass spectrometry (In-solution digestion followed by Multi-dimensional Protein Identification Technology): This service includes trypsin digestion followed by an extended nano-RP-LC-MS/MS analysis for medium complexity samples (3 hour). For more complex samples, 2D-LC separation can be performed followed by fraction collection, desalting, standard 90 minute RP-LC-MS/MS analysis of each fraction, database search using either X!Tandem/TPP or Proteome Discoverer 2.1 (SEQUEST) and delivery of results (either as an e-mail link or an excel file format). The Investigator can decide the number of fractions to be analyzed after consultation with the laboratory manager. Longer gradients are also available at additional cost.
Identification of post-translational modifications:As post-translationally modified protein is only a small fraction of the total protein content and the ionization of modified peptide(s) is often suppressed in presence of huge number of unmodified peptides, identification of PTM sites require enrichment of modified peptides. Some well established methods for enrichment of phosphopeptides and glycopeptides are available (see below).
Phosphorylation - Metal Oxide Affinity Chromatography (TiO2).
Glycosylation - Based on Solid Phase Extraction of Glycopeptides (SPEG)
Parallel Reaction Monitoring (PRM) for quantification of proteins and post-translational modifications: PRM approach is employed for validating (eg. a potential biomarker identified during discovery phase) and/or more accurate quantitation of an analyte in a large cohort of samples. The instrument is set to isolate only analyte(s)-of-interest (i.e., specific m/z), fragment (HCD) and acquire MS/MS. This configuration can improve the sensitivity of detection and dynamic range of quantitation of the analyte. For absolute quantification, the experiment involves spiking-in a known amount of heavy-isotope labeled analyte into the peptide mixture derived from relevant sample matrix and monitoring both endogenous and heavy-isotope labeled peptides. Since the heavy-isotope labeled peptide is physico-chemically identical (except mass) to the endogenous peptide, they co-elute and the area under the curve (AUC) can be used to determine the concentration of the endogenous peptide. As PRM process requires optimization of experimental and data analysis pipelines, please contact the PRF beforehand to discuss the feasibility, sample requirements and cost of analysis.
Data-Independent Acquisition (DIA):
IMPORTANT NOTE(S):
All our instruments use electrospray ionization (ESI) for introducing the sample into the mass spectrometer and are less tolerant to several buffer components (salts, detergents etc). While some of these can be removed using additional cleaning steps, these will result in loss of sample. To avoid these steps if possible, the Investigator is encouraged to discuss the sample preparation method with the laboratory manager beforehand.
Most of the above services (except identification of Ubiquitination sites) can be performed using alternative enzyme. If enzymes other than trypsin are needed, the Investigator will provide the appropriate sequencing-grade enzyme.
All kits/reagents needed for PTM enrichment (such as TiO2 or ZIC-HILIC) or quantitative profiling (such as ICAT, iTRAQ, TMT or heavy labeled synthetic peptides necessary for MRM) will be provided by the Investigator.
Please review the Submission Guidelines for information on sample preparation that is necessary for proteomic analysis by tandem mass spectrometry.
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ON THE COVER
Breast team reviewing a patient's slide. (From left to right) Ghassan Allo, Fellow; Laura Walters, Clinical Lecturer; Celina Kleer, Professor. See Article Photography by Elizabeth Walker
Inside Pathology is an newsletter published by the Chairman's Office to bring news and updates from inside the department's research and to become familiar with those leading it. It is our hope that those who read it will enjoy hearing about those new and familiar, and perhaps help in furthering our research.
Inside Pathology is an newsletter published by the Chairman's Office to bring news and updates from inside the department's research and to become familiar with those leading it. It is our hope that those who read it will enjoy hearing about those new and familiar, and perhaps help in furthering our research.
Collaborates between Wayne County and the Department of Pathology and Social Work at U-M are imporving the lives of patient families and the faculty and staff who serve them, becoming a model for the future.
For over 60 years, photpographers have been on staff to provide imaging services for Pathology, covering departmental events, documenting research, and more. Go back in time through historical photos.
Director of Autopsy and Forensic Services, Dr. Jeffrey Jentzen, reflects on his career, beginning with his training in Minneapolis in the early ‘80 and including high profile cases such as the Jeffrey Dahmer serial killings.
In December, 2015, the Board of Regents approved the design for the Clinical Pathology Laboratories Relocation and Renovation project. Senior Project Manager, Christine Baker, explains how Lean Facility Design is being used to involve faculty and staff in creating the plans for their new workspace.
ON THE COVER
Dr. Sriram Venneti, MD, PhD and Postdoctoral Fellow, Chan Chung, PhD investigate pediatric brain cancer. See Article Photography by Dustin Johnston
Editorial Team
Robin Kunkel Barbara McKenna, MD
Vashni Santee
Elizabeth Walker
Prinicipal Photography
Dustin Johnston
Elizabeth Walker
Layout Design
Brent Temple
Contributors
Christine Baker Lina Shao, PhD
Leslie Stainton
Sara Talpos
Elizabeth Walker
newsletter
INSIDE PATHOLOGY
About Our Newsletter
Inside Pathology is an newsletter published by the Chairman's Office to bring news and updates from inside the department's research and to become familiar with those leading it. It is our hope that those who read it will enjoy hearing about those new and familiar, and perhaps help in furthering our research.
Dr. Siram Venneti's lab explores the interface of metabolism, epigenetics and brain development in order to better understand and eventually treat childhood cancer.
Cancer cytogenomic arrays detect genomic legions in tiny amounts, resulting in big impacts on patient care, including more targeted therapy for pediatric brain tumors.
Editorial Team
Robin Kunkel
Christine Rigney
Vashni Santee
Elizabeth Walker
Prinicipal Photography
Dustin Johnston
Layout Design
Brent Temple
Contributors
Christine Baker Rohit Mehra, PhD
Leslie Stainton
Sara Talpos
newsletter
INSIDE PATHOLOGY
About Our Newsletter
Inside Pathology is an newsletter published by the Chairman's Office to bring news and updates from inside the department's research and to become familiar with those leading it. It is our hope that those who read it will enjoy hearing about those new and familiar, and perhaps help in furthering our research.
CONTENTS
Chairman’s Corner
An update from the Department Chair from 2017-2018
Rohit Mehra, MD, saw patient after patient with metastatic therapy resistant cancer. As a pathologist, he knew something unconventional was needed to understand why the patient's cancer would not respond to treatment.
Question & Answer: Helping Patients and Families in Ghana—A Staff Perspective
Senior Histotechnologists, Stephanie Allen, descibes her experiences as she accompanied Dr. Richard Lieberman and his team in bringing quick diagnoses to GYN patients in Ghana.
John H. Finger, MD got to know his father through walks in the Department of Pathology. Now, a gift from the family is inspiring future leaders in the field of forensics.
The story of how Kathleen R. Cho, MD, the Peter A. Ward Professor of Pathology, created a career in which she excels at diagnostics, research, and administration.
Alumni Story: Hidden Gems
Catch up with U-M residency program alumna, Dr. Güliz Akdaș Barkan and learn how the mentorship of Dr. Bernard Naylor shaped her career.
To solve one of the most complex challenges of the department's move to north campus, pathology informatics put together a team to create a new specimen tracking applications, in house.
ON THE COVER
Residents Ashley Bradt (left) and William Perry work at a multi-headed scope in our new facility. Photography by Dustin Johnston
Inside Pathology is an newsletter published by the Chairman's Office to bring news and updates from inside the department's research and to become familiar with those leading it. It is our hope that those who read it will enjoy hearing about those new and familiar, and perhaps help in furthering our research.
CONTENTS
Chairman’s Corner
An update from the Department Chair from 2018-2019
Duane Newton, PhD, reflects on how communication, determination, and commitment have led to the best possible outcomes for patients and the department through the Pathology Relocation and Renovation Project (PRR).
Sheryl Silver became an advocate for women’s health after her sister’s diagnosis of ovarian cancer. Now, a gift from the Silver Family Foundation is funding research at Michigan Medicine.
Our faculty want to give High School students the best chance to learn about pathology.
Living Big
In January, the Department of Pathology lost Dennis Serras who was a dear member of the Patient and Family Advisory Council (PFAC). What was his viewpoint and how did he help?
ON THE COVER
Dr. Kristine Konopka (right) instructing residents while using a multi-headed microscope. Photography by Camren Clouthier
Inside Pathology is an newsletter published by the Chairman's Office to bring news and updates from inside the department's research and to become familiar with those leading it. It is our hope that those who read it will enjoy hearing about those new and familiar, and perhaps help in furthering our research.
CONTENTS
Chairman’s Corner
An update from the Department Chair from 2019-2020
A Holistic Approach
Now in its 35th year, and tasked with a range of daunting responsibilities, the Division of Education Programs is key to "having the best pathology education department in the country," says new director Carol Farver, MD.
Throwing Open the Doors to Pathology
The new medical school curriculum offers students a unique opportunity to gain exposure to the clinical practice of pathology.
First-Class Team Guides Trainees to Success
When third-year medical students are deciding where they want to spend their residency, our department has a dedicated team ready to guide them through the process.
Towards the Future of Biomedical Graduate Education
Dr. Zaneta Nikolovska-Coleska gives her perspective on the Molecular and Cellular Pathology Graduate Program, and insights as to it’s growing future.
A Metric Ton of Challenges
After landing in the emergency room with acute chest syndrome, patient Jamison Lundy had his first experience with apheresis and gained full trust in Michigan Medicine.
Embracing the Chaos
Allecia Wilson, MD, grew up in a poverty-stricken area in Detroit and had a career in the military before a eureka moment led her to pathology. The Director of Autopsy and Forensic Services shares thoughts on mentorship, family, and more.
Renaissance Man
U-M Pathology Alumni John Goldblum has developed an impressive resume since attending medical school, but reflects how his love of the field was inspired by his teachers.
Fellowship Q&A
There are a number of questions that surround being involved in a fellowship. We interview four of our own about its advantages.
ON THE COVER
Patient specimens poised for COVID-19 PCR testing. Photography by Camren Clouthier / Digital Art by Brent Temple
Contributors
Christine Baker
Camren Clouthier
Jason Keech
Zander Tolyn
Anne Van Veen
newsletter
INSIDE PATHOLOGY
About Our Newsletter
Inside Pathology is an newsletter published by the Chairman's Office to bring news and updates from inside the department's research and to become familiar with those leading it. It is our hope that those who read it will enjoy hearing about those new and familiar, and perhaps help in furthering our research.
CONTENTS
Chairman’s Corner
An update from the Department Chair from 2020-2021
The SARS-CoV-2 virus brought laboratory testing to the headlines. Learn how Michigan Medicine Pathology responded to this unprecedented challenge.
Leading the Charge
Leadership at all levels engaged in the fight against COVID — a behind-the-scenes look at what was required to keep patients and colleagues safe while providing exceptional care.
The Yin and the Yang of Research in the COVID Era
As COVID closed down research labs, researchers sgifted focus to new areas of research, publications, and grantsmanship.
Flexibility is the Key to Activation
More than 18 months into the renovation effort at University Hospital and University Hospital South, flexibility has been key to the ever-changing environment.
A Journey Through Chemistry and Medicine
A faculty perspective from the department's Dr. Carmen Gherasim, who offers a unique insight into her personal life, career endeavors, and staying afloat during the COVID-19 pandemic.
Facing Down COVID One Patient at a Time
Pathology phlebotomists discuss their experiences working with patients through the COVID pandemic, balancing compassion and safety.
Schnitzer Lectureship and Resident Wellness Funds
Honoring the legacy of Dr. Bertram Schnitzer and supporting our pathology residents one gift at a time.
Expertise in Reference Laboratory Services
MLabs, established in 1985, functions as a portal to provide pathologists, hospitals. and other reference laboratories access to the faculty, staff and laboratories of the University of Michigan Health System’s Department of Pathology. MLabs is a recognized leader for advanced molecular diagnostic testing, helpful consultants and exceptional customer service.