Methods employed in the lab

The multidisciplinary and collaborative nature of our research requires a wide array of analytical capabilities.

Pipetting Samples
Science
Scientist in the Lab

Metabolomics

Global untargeted or targeted with absolute quantification

Akin to genomics or proteomics, true metabolomics aims to understand all of the small molecules in biological systems. Many "metabolomics" labs quantify a relatively small range of well characterized metabolites. Through the use of ultra-high resolution untargeted metabolomics we first quantify all of the ionizable small molecules in biological material. Molecules of interest can then be identified by methods such as: stepped fragmentation, high resolution ion mobility, or Electron Activated Dissociation (EAD via E-I-E-I-O). Validation can be performed by absolute quantification of metabolites of interest. You can read a recent collaborative work on human samples here. 

Single cell proteomics, metabolomics and lipidomics

We are pioneers in single cell mass spectrometry

If you've found this website, chances are you're interested in single cell measurements by mass spectrometry. We have access to advanced cell and liquid handling technologies such as the SciFlex Arrayer and CellenOne systems. Our work detailing the first quantitative analysis of protein post-translational modification in single human cells is currently in review. You can find an early preprint here. We are continuing to push forward with single cell metabolomics and lipidomics manuscripts in preparation. Preprints coming soon.

Immunopeptidomics

Characterization of new cell surface neo-antigens

The need for new methods to discover neo-antigens for personalized medicine led to the co-awarding of the LDER grant in 2018. We have continued to modernize immunopeptidomics with new instrument and computational pipelines. Using a Cloud computing approach in collaboration we identified a new class of neo-antigens arising from "non-coding" sections of the DNA. While controversial (and difficult to publish) at the time, these results have since been independently verified.

 

Hardware

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Q Exactive

Ultra high resolution mass spectrometry with custom modifications

The Q Exactive is one of the world's most popular mass spectrometers today -- for very good reasons. Our Q Exactive is capable of 200,000 resolution and can be operated through the vendor software or through a custom interface allowing the implementation of new instrument methods. The Q Exactive is adept at global metabolomics through antibody drug conjugate characterization, and everything in-between.

TIMSTOF Flex + MALDI

Proteomics, lipidomics and mass spectrometry imaging aided by ion mobility

The TIMSTOF Flex is our lab workhorse. This ceiling altering tool completed nearly 4,000 LCMS runs and over 700 hours of MALDI-imaging runs in the first 18 months following installation. Up to 6,500 proteins have been quantified in a single run from human samples prepared in-house (and more from commercially prepared standards, but those don't count).

ZenoTOF 7600 with electron activated dissociation

Inline zenotrapping provides unprecedented dynamic range in high resolution hardware

Through a collaboration with SCIEX, we obtained one of the first ZenoTOF instruments in the US. This compact Q-TOF is capable of over 120 scans/second with inline ion accumulation. Surprisingly, a novel Electron Activated Dissociation (EAD) method has proven immensely powerful in the characterization of protein post-translational modifications in a wide array of contexts.

 
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TIMSTOF Single Cell

The most sensitive high resolution mass spectrometer ever built? 

The TIMSTOF Single Cell couples the power of the TIMSTOF Flex with a new ion front end providing unprecedented levels of sensitivity. Over 1,000 proteins can be identified in 30 minutes from 200 picograms of commercial K562 digest. While this should never been extrapolated to the results obtained for a 200picogram single cell, the sensitivity of this instrument is providing amazing levels of analysis in actual human cells.

CellenOne

Sort and prepare single cells by gentle microscopy based approaches

The University purchased us the CellenOne placed this in our Single Cell and Transcriptomics Core facility. Managed by experts in single cell analysis and automation, this is an invaluable new tool for difficult or low-abundance cell types. 

SciFlex Arrayer S3 picoliter liquid handling

When absolute precision in liquid handling is paramount

This SciFlex in our department is the property of our collaborators in the Netz Lab and is used for focused projects requiring the handling of picoliter volumes.