Duke Proteomics and Metabolomics Core Facility Positions


The information below comes from Dr. Arthur Moseley, Director of the Duke Proteomics and Metabolomics Core Facility. Arthur is recruiting to fill two open positions. The primary focus for each would be in metabolomics, which is now over 50% of their total business. Arthur’s contact information is provided below.

  1. Laboratory Research Analyst II – https://career4.successfactors.com/sfcareer/jobreqcareer?jobId=126108&company=dukeuniverP1
    1.  4+ years’ research experience past BS, with BS/MS/PhD scientists of interest. 
    2. The four years’ experience is offset for MS and PhD candidates based on the years they spent for their post-BS degree.
  2. Senior Research Scientist – https://career4.successfactors.com/sfcareer/jobreqcareer?jobId=136449&company=dukeuniverP1
    1. 10+ years’ experience past PhD, either in industry or academia. 
    2. Note this position is the highest-level full time staff scientist position at Duke. The School of Medicine has made Research Professor appointments for four PhD scientists with 10+ years of experience in our lab, but if such an appointment were to be made for a new scientist in our lab, it would be after the candidate accepts the position at Duke and has had a chance to work with a few key PIs. Such appointments are made by individual Basic Sciences or Clinical Sciences Department in the School of Medicine.

A Facilities and Resources description for the Duke Proteomics and Metabolomics Core Facility is attached.

Information about the research:

Duke Proteomics and Metabolomics Core Facility (http://www.genome.duke.edu/cores/proteomics/)

In February 2007 the Duke School of Medicine created a Proteomics Core Facility to provide protein characterization resources for the Duke Research Community. This Facility was designed to provide all needed capabilities for mass spectrometry based proteomics. In 2013 the Facility expanded its LC-MS/MS services to include qualitative and quantitative metabolite characterization, and in 2014 the Facility’s name was formally changed to the Duke Proteomics and Metabolomics Core Facility.  The Facility is staffed with ten scientists (five PhDs, four of whom are Research Professors in the School of Medicine) with a combined experience of over 160 years in the analysis of peptides, proteins, and small molecules by liquid chromatography-tandem mass spectrometry.

Duke Proteomics and Metabolomics Facility Analytical Equipment

The Proteomics and Metabolomics Core Facility provides capabilities for mass spectrometry based proteomics and metabolomics for identification and quantitation, including biomarker discovery and biomarker verification experiments. The DPMCF (https://genome.duke.edu/cores /proteomics) is located in a new (2017) ~8,100 sq. ft. laboratory in the Chesterfield Building, one custom built for mass spectrometry based proteomics and metabolomics.  In this space there is an instrument lab (~4,300 sq. ft.), with stations for 15 mass spectrometers, including all requisite UPS power, UHP gases, GB internet and telephone lines. and instrument and pump exhausts. There is a ~1,100 sq. ft. wet lab, which includes two fume hoods, two laminar flow hoods, two biosafety cabinets (one being Class 2). There are separate rooms for equipment repair, equipment/gas tank storage, a dedicated UPS (with emergency power backup), data workstation space, five offices and 9 cubicles.

For qualitative identifications and biomarker discovery experiments (‘omic-scale qualitative and quantitative analyses), the laboratory is equipped with seven high resolution accurate mass LC-MS/MS systems. Four of these systems are hybrid quadrupole-orbitrap tandem mass spectrometers – a Fusion Lumos Tribrid with ETD, a Fusion Lumos Tribrid with ETD and UVPD, an Exploris 480, and a Q-Exactive Plus (Thermo). The other three systems are hybrid quadrupole time-of-flight tandem mass spectrometers (one Synapt G1, and two Synapt G2 High Definition Mass Spectrometers, Waters). There are two FAIMS Pro LC-MS/MS interfaces for use with the Lumos and Exploris systems. For proteomic biomarker verification experiments, targeted metabolomics and pharmacokinetic experiments, targeted mass spec quantitative experiments are performed on ultra-high performance UPLC systems coupled to a triple quadrupole tandem mass spectrometer (one 6500+ QTrap (Sciex), one Waters Xevo TQ-XS and two Waters Xevo TQ-S). For these experiments, data acquisition is accomplished using LC-MS/MS with Multiple Reaction Monitoring. Each of these mass spectrometers is coupled to a dedicated UPLC system; indeed, there are four Waters nanoAcquity LC systems, two multidimensional Waters nanoAcquity LC/LC systems, one Acquity-M Class LC/LC, four Acquity LC systems (Waters) and an ExionLC (Sciex) . There is also an I-Class Acquity coupled to a Waters’ Fraction Manager (two 96 well plates) for offline fractionation (high pH RP or SCX). The laboratory has the tools needed for enrichments (chemical and/or antibody-based) of sub-proteomes based on Post-Translational Modifications, including glycosylation, phosphorylation (pST, pY, pSTY global or kinase motif-specific enrichments), acetylation, ubiquitination, methylation, acylation, and S-nitrosylation, followed by qualitative and quantitative characterization using LC-MS/MS. For metabolomic studies, the DPMCF has targeted assays for >850 metabolites, including amino acids, biogenic amines, lipids, bile acids, oxylipins, hydroxycholesterols, fatty acids (long chain and short chain), purines/pyrimidines, and energy cycle metabolites. Recently, the DPMCF has acquired a liquid handling robot (opentrons OT-2) and a Dionex Ultimate nanoscale LC system specifically for research in single cell proteomics.

Proteomics and Metabolomics Core Facility Dedicated Informatics Infrastructure

Data processing is accomplished using eight DPMCF dedicated ‘virtual cluster’ servers, three high performance local workstations and a dedicated, mirrored data storage system. Protein identifications from MS/MS spectra are accomplished using either of three search engines – Mascot Server 2.5 (Matrix Sciences), Spectronaut/Pulsar (Biognosys), and MaxQuant (Mann Lab.In addition, Mascot database searching is further supported by the use of the Mascot Daemon and Mascot Distiller, providing an automated pipeline for processing raw qualitative mass spectrometry data into confident protein identifications. An additional qualitative and quantitative data processing pipeline is built around Proteome Discoverer 2.5 (Thermo). Importantly, scientists in our lab (Soderblom and Waitt) have created a custom R-script-based data processing pipeline. The Skyline program (MacCoss Lab, U Wash.) is used for processing targeted proteomics and metabolomics experiments. For quantitative ‘omic metabolomics Progenesis QI (Waters) is used. Public databases of metabolite identifications are used for metabolite work, including the Scripps METLIN database. Targeted metabolite quantitative data analysis is performed using TargetLynx package for LC-MS/MS  (Waters) or MultiQuan (Sciex), and for the Biocrates assays, these are combined with the MetIDQ software (Biocrates, Inc).  All data from Biocrates is stored in a dedicated Oracle database which is backed up and mirrored. Label-free quantitative data processing of DDA data using accurate mass-and-time-tag alignment is accomplished using Proteome Discoverer software (Thermo) running on two dedicated workstations, each with 32 processing cores and 64 GB of RAM. For DIA experiments, Spectronaut/Pulsar (Biognosys) is used, running on an identical dedicated workstation. For data visualization and for data return to Resource collaborators, the Resource uses Proteome Software Scaffold and Scaffold PTM. For data acquisition there are 11 instrument control PCs. In addition, each staff member has their own laptop PC and/or desktop PC. For raw data storage, the Resource has 115 TB of dedicated ‘enterprise-quality’ primary data storage which is maintained by Duke’s Office of Information Technology. The lab uses the secure web-based “GCB Express” data repository for processed data storage/distribution from projects. “Express” has been developed by GCB programmers to ease data production activities in the Cores. Express Data Repository holds data sets produced by core facilities and uploaded by Duke Researchers and their collaborators. It is a true repository, in that data cannot be changed once it is put into Express. Data integrity features include data “fingerprinting” on upload, and strict access controls managed by data owners.

Additional analytical resources in the Facility available include:

Conventional HPLC system for biofluid immunodepletion and sample fractionation; 96-well Viaflo96 automated pipettings system; liquid handling robot (opentrons OT-2); two N2 plate driers; isoelectric focusing offgel system for prefractionation of complex samples; gelfree molecular weight separation system for prefractionation of complex samples; Thermomixers (x4); chilled analytical centrifuge; high speed microcentrifuge (x2); speed-vacuum centrifuge; lypholizer; 1D gel rigs (x2); high resolution gel image scanner; image processing software; 96-well plate reader; microbalance; pH meter; freezers (-80C (x4), -20C (x2), and -4C).