Duke Proteomics and Metabolomics Core Facility Positions

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).

Funding Opportunities

PAR-21-253: Identification and Characterization of Bioactive Microbial Metabolites for Advancing Research on Microbe-Diet-Host Interactions (R01 Clinical Trial Not Allowed)

and

RFA-DK-21-014:  Identification and Characterization of Bioactive Microbial Metabolites for Advancing Research on Microbe-Diet-Host Interactions Knowledgebase Management Center (U24 Clinical Trial Not Allowed)

Postdoctoral Position available at NIEHS

Molecular Epidemiology (Metabolomics/Molecular Genomics) of Environmental Health Disparities in Cardiovascular Disease

Position Description: A postdoctoral position is available in the Mechanistic Toxicology Branch in the Division of the National Toxicology Program (DNTP) at the National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, North Carolina. This is a cross-divisional (Division of Intramural Research, Division of the National Toxicology Program, and Division of Extramural Research and Training) project that is focused on investigating environmental health disparities in cardiovascular disease. Candidate will be mentored by a multi-disciplinary team with primary co-mentors (David Crizer and Alan Jarmusch). The successful candidate will have the opportunity to use a variety of techniques such as untargeted metabolomics and molecular genomics to identify a broader profile of metabolic-type factors to contribute to our current understanding of disparate hypertension risk across racial groups.

The Research Triangle Park area and the surrounding educational institutions provide excellent networking and career development opportunities. Stipends are regulated by the institute’s intramural funding policy and can be found here. NIH is dedicated to building a diverse community in its training and employment programs.

Qualifications:

· Doctoral degree in chemistry, biochemistry, molecular epidemiology, or closely related discipline

· Experience in liquid and/or gas chromatography-mass spectrometry (LCMS/GCMS) based metabolomics is preferred

· Interest in and ability to work collaboratively with individuals from different professional disciplines and personal backgrounds

To Apply:

Email david.crizer@nih.gov a single PDF containing:

· Cover letter

· Curriculum vitae

· Names of three references with contact information (email and phone number)

Applications will be evaluated as they are received until the position is filled. Preferred start date is September 13, 2021.

Cell lines for generation of exposome metabolites

The NIEHS-funded Compound Identification Core (CIDC) at Emory University has pioneered the use of laboratory-generated xenobiotic metabolites for use in annotation of the human exposome.  We are now making available a panel of cytochrome P450-expressing cell lines to academic researchers in metabolomics and xenobiotic metabolism.

These cell lines are prepared by lentiviral transduction of human hepatoma Huh7 cells and maintained by selection with blasticidin.  Cytochrome P450 enzymes are C-terminally tagged with the V5 peptide and can be detected or precipitated with commercially available antibodies to V5.  All listed enzymes have been verified to be catalytically active in the cells.  The lentiviral plasmids with the cloned enzymes are also available.

Recipients will be expected to provide a FedEx account number to pay for shipping.  If a large number of lines are requested, if demand is unexpectedly high, or if international shipping is required, recipients will be informed prior to shipment of any additional charges needed to recover costs. 

CYP1A2

CYP2A6

CYP2B6

CYP2C8

CYP2C9

CYP2C19

CYP2D6

CYP2E1

CYP2J2

CYP3A4

CYP3A5

CYP3A7

Send requests or enquiries to Eddie Morgan etmorga@emory.edu.  Additional cell lines are under construction or testing.

Supported by grant U2CES030163 from the National Institute for Environmental Health Sciences

NIH Common Fund for Metabolomics

The goal of the Common Fund’s Metabolomics program is to inform basic, translational, and clinical research. Metabolomics is the scientific study of the chemical reactions that occur in organisms, cells, or tissues. Each reaction produces small chemicals called metabolites, which play critical roles in keeping our cells healthy and functioning properly. As these different chemical reactions and the metabolites they produce are unique to every individual, by improving metabolomics methods and making them more accessible to different researchers it may allow for more personalized diagnosis of disease and treatment methods moving forward.

Metabolomics Workbench

The Metabolomics Common Fund’s National Metabolomics Data Repository(NMDR), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego, has developed the Metabolomics Workbench. The Metabolomics Workbench serves as a national and international repository for metabolomics data and metadata and provides analysis tools and access to metabolite standards, protocols, tutorials, training, and more.

The data and other resources developed by the Common Fund Metabolomics program are managed by the Data
Repository and Coordinating Center (DRCC) at the San Diego Supercomputer Center, University of California, San
Diego. The DRCC makes these materials publicly available through the Metabolomics Workbench website.

Omics Discovery Index

The Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics).

Most data in the Datatsets Discovery Index can be accessed programmatically using a RESTful API. The API implementation is based on the Spring Rest Framework. Web-browsable API The OmicsDI API is web browsable, which means that: The query results returned by the API are available in JSONformat and also XML. This ensures that they can be viewed by human and accessed programmatically by computer. The main RESTful API page provides a simple web-based user interface, which allows developers to familiarize themselves with the API and get a better sense of the OmicsDI data before writing a single line of code.

OmicsDI project has been developed on GitHub, you can check or contribute to our development here

Request for Applications: Pilot and Feasibility Projects

The Metabolomics Consortium Coordinating Center (M3C) together with the Southeast Center for Integrated Metabolomics (SECIM) requests applications for up to 12-month pilot projects.

The goal of the NIH Common Fund’s Metabolomics program (see https://commonfund.nih.gov/metabolomics) is to inform basic, translational, and clinical research. Metabolomics is the scientific study of the chemical reactions that occur in organisms, cells, or tissues. Each reaction produces small chemicals called metabolites, which play critical roles in keeping our cells healthy and functioning properly. As these different chemical reactions and the metabolites they produce are unique to every individual, by improving metabolomics methods and making them more accessible to different researchers it may allow for more personalized diagnosis of disease and treatment methods moving forward.  In order to catalyze science around the role of metabolomics in human health, the Metabolomics program supports research to establish a long standing national public repository for metabolomic data, to overcome technical hurdles in analyzing and interpreting metabolomics data, including the ability to determine metabolite identities, and to develop best practices and guidelines with help from the national and international metabolomics communities to promote accuracy, reproducibility, and re-analysis of metabolomics data. 

Specific objectives of the current phase of the NIH Metabolomics Program include: (1) establishment of a National Metabolomics Data Repository (NMDR) which is widely adopted by the national and international metabolomics community, supports facile data and metadata deposition and access for re-use, and provides a means for citing the data and its provenance; (2) addressing key challenges in analyzing and interpreting metabolomics data by catalyzing the field of compound identification to dramatically increase the number of identified biomedically-relevant, metabolites in metabolomics spectra; (3) addressing key challenges in analyzing and interpreting metabolomics data by developing novel tools to facilitate metabolomics data analysis and interpretation; and (4) community engagement and program coordination to generate consensus and achieve wide-spread adoption of standards and guidelines for best-practices and data sharing in metabolomics.

M3C is the Metabolomics Consortium Coordinating Center of the NIH Common Fund’s Metabolomics program; the mission of the M3C is to serve as a catalyst for the advancement of metabolomics in biomedical research and clinical care by engaging the diverse range of stakeholders, organizing the consortium, and promoting its work. Stakeholder engagement includes symposia to identify roadblocks in the use of metabolomics and suggest approaches leading to remediation. Pilot and Feasibility awards focus on biomedical research projects new to the use of metabolomics.  Consortium work is organized through a web portal (see https://metabolomics.info/about/), providing access to all consortium resources, including access to datasets in the National Metabolomics Data Repository, and tools developed by the Metabolomics Data Analysis and Interpretation Tools awardees.  M3C further organizes the work of the consortium by facilitating on-line and in-person meetings of governance groups and workgroups.  M3C promotes the work of the consortium through social media (@metabinfo), its web portal, presentations at scientific meetings, and distribution of consortium standards, policies, procedures, protocols, best practices, and guidelines. The work of the coordinating center, and of the metabolomics consortium, will lead to improved human health through basic research findings, improved laboratory practices, and translation to clinical research and care.

The Southeast Center for Integrated Metabolomics at the University of Florida (SECIM, see http://secim.ufl.edu/) was established in the first phase of the Common Fund’s Metabolomics program, and continues to provide world-class metabolomics services and research through UF’s Clinical and Translational Sciences Institute, as well as serving as the home of M3C. Pilot and Feasibility Awards are intended to support projects that will provide preliminary data for new extramural grant application submissions. The review process will emphasize innovation and the potential of the work to have a significant impact on an important biomedical research problem.

Purpose

The overarching goal of the M3C will be the promotion of metabolomics as a key component of biomedical research (basic, clinical, and translational) and clinical care. The Pilot and Feasibility Program is a part of stakeholder engagement meant to enhance metabolomics research by providing support for investigators new to the metabolomics field, the development of new teams and partnerships, and high-risk/high-impact research. This program will focus on awards for the generation of metabolomic data from samples in biomedical research where previous work is rare or nonexistent. The program also aims to open additional areas of biomedical research to the use of metabolomics by specifically inviting biomedical researchers to apply. The Pilot and Feasibility Program aims to form new multidisciplinary collaborations that will enhance the integration of new techniques that benefit multiple investigators; it also aims to promote the consortium objectives (compound identification and data analysis). Applications from basic, translational, and clinical researchers are encouraged. Extending the collaborative nature of research projects by matching funds from other mechanisms is encouraged.

Eligibility

All basic, translational, or clinical investigators located at institutions within the United States who are eligible to apply as a PI for NIH grants are welcome to apply for M3C pilot awards. Young investigators and investigators who are new to the field of metabolomics are especially encouraged to apply.

Application Procedure

Applications should be submitted using the instructions that can be found on the M3C’s website (http://metabolomics.info). PHS 398 format is required.  Deadline date for receipt is Friday, April 16, 2021.  NIH application guidelines will be followed.

Applications must include the following elements:

  • Cover Sheet
  • Abstract
  • Budget and budget justification
  • NIH biographical sketches
  • Eligibility statement
  • Research Strategy (5 pages maximum) must include:   Specific Aims, Background, Significance, and Rationale for the use of metabolomics, Impact, Preliminary Results (if any), Experimental Approach
  • Plans for future funding
  • References
  • Protection of human and/or animal subjects

Additional Considerations

M3C is dedicated to funding as many unique and innovative projects as possible with goals of expanding the range of biomedical applications of metabolomics and advancing metabolomics technology in the identification of metabolites.  Impactful applications of $15,000 or less will typically receive preference over those with higher budgets. Requests for salary for the Principal Investigator or personnel, laboratory or extramural services outside of M3C are not permissible. All funds will be awarded in credit toward services performed at SECIM, including study design and some statistical support, or in payment for the project’s materials and supplies.

M3C specifically encourages applications that form scientific partnerships, span several scientific domains, include trainees, and benefit multiple investigators. The role of the PI, trainee(s), and collaborators affiliated with the project should be clearly defined. The names of all funded investigators will be posted on the M3C website. Grantees must acknowledge the M3C NIH grant U2CDK119889 in any abstracts, presentations, or publications resulting from supported studies and provide quarterly progress reports, a final report, and an annual report that includes publications and new grant awards. As mandated by the NIH Common Fund Metabolomics Program, all resulting metabolomics data and associated metadata will be publicly deposited in the National Metabolomics Data Repository (NMDR).

Application Review

All submitted applications will be internally reviewed by the M3C Steering Committee for technical feasibility and compliance with the above requirements and formats. External reviews will use the NIH review scoring criteria and scores. Final funding decisions will be made by the Metabolomics Program Executive Committee.

Application receipt deadline: April 16, 2021

Earliest funding start date: June 14, 2021

Interested investigators are encouraged to discuss their applications with SECIM Faculty:

Proposals must be submitted by no later than 5:00 p.m., April 16, 2021, to Dr. Alisha Mitchell-Roberts, amitch@ufl.edu

Application Instructions (docx file)

Application Forms


Abstract (docx format)

Budget (docx format)

Justification (docx format)

NIH Biographical Sketch (docx format)

Eligibility Statement (docx format)

Research Strategy (docx format)

Plans for Future Funding (docx format)

References (docx format)

Protection of Human and Animal Subjects (docx format)