Ask the Experts: Ensuring High-Quality Proteomic Studies with Core Lab Resources

ABRF-TY-180x150-2017

Date: October 10, 2017
Time: 1:00 pm Eastern Time

REGISTER

This online, interactive seminar will answer researchers’ most pressing questions about how to gain outstanding research results from proteomic studies. Researchers and clinicians are increasingly adopting proteomics as a go-to method for gaining biological insights and direction. Proteomic core labs are shared resources with the expertise and instrumentation to carry out these specialized studies. Collaboration between researcher and proteomic core combines the expertise and leverages the strengths of both parties. This webinar will provide building blocks on which to jumpstart or strengthen this key relationship.

From study design and sample preparation through data analysis, result interpretation, and overall reproducibility, our panelists will answer your essential questions about setting up and carrying out high-quality proteomic studies. This practical insider info will help researchers and cores to work together and effectively move research forward.

Presenters:

Emily Chen, PhD
Director of Proteomics Shared Resource
Herbert Irving Comprehensive Cancer Center
Assistant professor of Dept. Pharmacology
Columbia University Medical Center, New York, NY

Brett Phinney, PhD
Director, Genome Center Proteomics Facility
University of California, Davis, CA

Scott Shaffer, PhD
Director, Proteomics and Mass Spectrometry Facility
Research Professor, Biochemistry and Molecular Pharmacology
University of Massachusetts Medical School, Shrewsbury, MA

David L. Tabb, PhD
Professor, Division of Molecular Biology and Human Genetics
Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa

REGISTER

Questions? Contact genomewebinars@genomeweb.com

GenomeWeb and the Association of Biomolecular Resource Facilities (ABRF) are partnering for the second year to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. Special thanks to the series sponsor, PerkinElmer

Press Release: The Nobel Prize in Chemistry 2017

Cool microscope technology revolutionizes biochemistry

We may soon have detailed images of life’s complex machineries in atomic resolution. The Nobel Prize in Chemistry 2017 is awarded to Jacques Dubochet, Joachim Frank and Richard Henderson for the development of cryo-electron microscopy, which both simplifies and improves the imaging of biomolecules. This method has moved biochemistry into a new era. Read more about this year’s prize…

New FASEB Report: Leveraging Shared Resources to Improve Research

A new report from the Federation of American Societies for Experimental Biology (FASEB), “Maximizing Shared Research Resources,” identifies the challenges encountered by shared research resources providers and users, and makes recommendations for improvement.

Shared research resources – from core facilities to living collections and national laboratories – make efficient use of funds and broaden researchers’ access to advanced technologies and materials. But shared resource providers face difficulties that limit their ability to offer cutting-edge services.

FASEB surveyed shared resource users and providers and identified four key areas for improvement:

Create better business models for shared resource facilities;

  1. Enhance funding programs that support facilities;
  2. Increase national awareness of shared resources;
  3. Connect researchers with institutional resources.

Click here to view the full report including the survey instrument and analysis of findings. For more information, contact Bethany Drehman, FASEB Senior Science Policy Analyst.

Cores: Part of the solution to experimental irreproducibility

Experimental reproducibility is rooted in many things; one of them being poorly validated antibodies. Numerous scientists have highlighted this problem for quite a few years, with this weakness making it into the public arena.  The NIH has taken a step forward by requiring a plan to authenticate key biological and/or chemical resources, among which are antibodies, as part of their research grant and mentored career development applications, but it is the scientific community that needs to develop and implement solutions. Several groups have taken up the charge to facilitate a cultural shift among the many players, among them, Global Biological Standards Institute (GBSI) and Biocompare. Last fall, GBSI ran a workshop entitled “Antibody Validation: Standards, Policies, and Practices” where key stakeholders from academia, industry, funding entities, and journals came to share perspectives and contribute to real and feasible solutions for validating antibodies. The ABRF was proud to sponsor and represent core facilities during these productive discussions of challenges. Participants worked together to map out a path forward through working groups to create a series of antibody validation guidelines for each of the seven most commonly used techniques. This summer, Biocompare stepped up to the plate by producing a very well framed and thought-provoking documentary on the role antibodies play in reproducible scientific endeavors, in which the ABRF was honored to participate.

Core facilities are particularly well positioned to expedite the process towards a better appreciation for this particular biological reagent class as well as to support researcher through a robust validation process. The scientists in core facilities can actively participate in moving antibodies off the list of irreproducibility contributors because they are the “boots on the ground”, working daily with scientists in research labs. We would like to use this blog post to facilitate a conversation within our network of how ABRF can be part of the solutions.  Reading the GBSI workshop report or viewing the Biocompare documentary are great starting points to begin thinking about the role of core facilities in the solution.  Then come back to the blog to share your thoughts and participate in our collective discussion, one that will hopefully lead to action within ABRF.

ABRF WIN2017 Phase 2 Study: Developing Procedures to Optimize Inter-Laboratory Reproducibility of LC-MS/MS-based Proteomic Analyses

June 30, 2017

Dear Colleague:

The 2017 ABRF Workflow Interest Network (WIN) is pleased to announce initiation of Phase 2 of a study to promote inter-laboratory reproducibility of quantitative proteomic LC-MS/MS analyses. Past studies of proteomic performance metrics have focused on the retrospective evaluation of collected data.  In this study we seek to identify data processing tools, including ID-free quality metrics, to support a proactive approach.

Participating laboratories will receive 2 samples: a mixture of peptide internal standards and a HeLa cell lysate digest.  A detailed protocol on how to run these samples will be provided when the samples are shipped.  We estimate it should take no more than 24 hours to complete the analysis.  Participating laboratories will submit raw files and complete a questionnaire of self-reporting parameters according to our instructions.  Results derived from the raw data will be de-identified to maintain the anonymity of the participating laboratories. Each participant will receive a unique identification number allowing them to compare their results with those of other participating laboratories.

The timeline for the study is as follows:

  • Sample requests accepted until August 1, 2017
  • Samples ship to participants starting August 1, 2017
  • Raw data files uploaded to the online repository by October 31, 2017
  • Results and analysis presented at the ABRF 2018 conference April 22-25, 2018, in Myrtle Beach, South Carolina, USA, then posted on the ABRF website.

To request a sample, please go to https://www.surveymonkey.com/r/H8XVSF3 and provide your shipping information before August 1, 2017. The WIN is eager to obtain data from a variety of different laboratories and mass spectrometry platforms, and encourages all mass spectrometry laboratories with an interest in proteomics and data quality metrics to participate.  However, because sample preparation and shipping involve a significant investment of time and money, Phase 2 is limited to 40 participants. The research group asks that you only request a sample if you are confident that you will be able to provide your raw files by the end of October.  We thank you for your support of the ABRF and look forward to your participation in this study.

Sincerely,

Sincerely,

The ABRF Workflow Interest Network
Emily Chen (chair), Achim Treumann, Alex Campos, LeeAnn Higgins, Sheng Zhang, Theresa McLaughlin, and Allis Chien (EB liaison)

 

ABRF Announces June 29 Webinar: Cross-Kingdom Standards in Genomics, Epigenomics, and Metagenomics

GW-Agilent-600x100-EH-3-17

Date: June 29, 2017
Time: 2:00 pm ET
REGISTER

Christopher Mason Weill Cornell Medical College

Christopher Mason – Weill Cornell Medical College

GenomeWeb and the Association of Biomolecular Resource Facilities (ABRF) are partnering for the second year to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. Special thanks to the series sponsor, PerkinElmer

The first in the series of online seminars, Cross-Kingdom Standards in Genomics, Epigenomics, and Metagenomics, will provide an overview of current standardization efforts in genomics, epigenomics, and metagenomics, with a focus on practical implementation considerations for researchers and labs. Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.

In this webinar, Christopher Mason of Weill Cornell Medical College will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review the computational methods for detection, validation, and implementation of these genomic measures.

More information on the GenomeWeb/ABRF 2017 Webinar Series is available here.

Scheduling conflict? You can still participate! All registrants will receive a link to view an on demand recording of the event.

Questions? Contact genomewebinars@genomeweb.com

ABRF Recognizes Volunteers During National Volunteer Week and Encourages All Members to Volunteer

Dear ABRF Members:

In recognition of National Volunteer Week, and on behalf of your Executive Board and Executive Director, Susan DeCourcey, I thank every one of our members for their continued commitment to the ABRF and all the volunteer work you do to support the advancement of core and research biotechnology laboratories. Your contributions of time, expertise and enthusiasm ensure the continued success of fulfilling on the ABRF’s mission, vision and goals. The work of the ABRF would not be possible without you!

If you are not currently active in the ABRF, one great way to network with your fellow ABRF members and to further develop your career is to participate in one of the various activities undertaken by your association.  Given the breadth of things we do, you will no doubt find something that aligns well with your interests.  Please look over the partial list of topics below. However, the best way to find something fulfilling is to send me an email indicating what you would be interested in doing with your colleagues. It can be related to any of the topics listed below or something developed organically. Also, the amount of time you choose to commit is totally up to you. You can participate in a discrete project with a defined end point, join a committee with a broader impact, or drive a research study.

Do any of these broad topics excite you?  Are there others?

  • Promote career development opportunities for our members
  • Develop educational opportunities, at and outside the annual meeting
  • Join with colleagues in your discipline to tackle common hurdles by joining a Research  Group
  • Be a voice for science advocacy
  • Build relationships between ABRF and like-minded organizations
  • Bring our journal JBT to the next level
  • Make the role of cores in Scientific Rigor and Reproducibility stronger and more prominent
  • Ask and answer technology-related questions through Research Group and Interest Network studies
  • Be a technical reviewer for journals
  • Strengthen and broaden ABRF-vendor relationships
  • Broaden our membership
  • Develop administrative resources
  • Keep your peers informed and engaged through social media and our website
  • Manage annual meeting logistics

I look forward to hearing from you.

Frances Weis-Garcia, ABRF President

frances.weis-garcia@my.abrf.org

 

Get Noticed at ABRF 2017!

The ABRF 2017 Program Committee is looking for your cool and exciting images to be displayed throughout the ABRF 2017 meeting space at the Town and Country Resort & Convention Center in San Diego, CA this March.

If your image is selected, it will be professionally printed (16” X 20”) and mounted.  As an added incentive for submitting, after the ABRF 2017 Annual Meeting your mounted prints will be mailed to your lab compliments of the ABRF!

Technical details:

  • Resolution 300 DPI at 16” X 20”
  • CMYK production, all color specifications will be matched to the closest 4-color process. Images without call-outs will be produced using the CMYK values contained in the digital file.

Formats:

  • Photoshop (.psd)
  • Encapsulated Postscript (.eps)
  • TIFF (.tif )
  • JPEG (.jpg)

Please email images by February 20 to richard.cole@health.ny.gov.

*If images are too large for email, contact Rich Cole for Dropbox instructions.

 

Take FASEB’s Shared Research Resources Survey and share your perspective as a user or provider!

The Federation of American Societies for Experimental Biology (FASEB) wants to learn about your experiences with shared research resources. Please complete this survey by March 2, 2017.

The questions in this 10-15 minutes survey focus on the following topics: (1) resource utilization and unmet needs; (2) the role of facilities in providing access to resources; (3) sources of funding and support for resources; (4) careers in resource provision and development as well as training on best practices. Your feedback will help inform FASEB’s policy positions and recommendations.

Please share this survey link widely with other biological researchers! FASEB is collecting responses from resource users and providers in the US. Survey link: http://www.surveygizmo.com/s3/3244931/FASEB-s-Shared-Research-Resources-Survey

ABRF Announces Executive Board Election Results

ABRF Members turned out in record numbers to elect two new members for the Executive Board.

Rich Cole, Research Scientist V, Director, Advanced Light Microscopy & Image Analysis Core, Wadsworth Center and Research Assistant Professor, Department of Biomedical Sciences, School of Public Health State University of New York and Nancy C. Fisher, PhD, Director, UNC Flow Cytometry Core Facility and Professor of Microbiology & Immunology, University of North Carolina at Chapel Hill were elected to serve a term of four (4) years on the Executive Board of ABRF. Their terms will commence immediately following the ABRF 2017 Annual Meeting in San Diego, California. Congratulations, Rich and Nancy!

The terms of Bill Hendrickson, President, and Paula Turpen, Treasurer, will conclude after the ABRF 2017 Annual Meeting. Thank you Bill and Paula for your outstanding leadership, hard work, and dedicated service to the ABRF and its membership.