R24GM141156

Seattle Quant: A Resource for the Skyline Software Ecosystem

Development on Skyline started in 2008 to fill a critical need for a software tool to enable targeted proteomics experiments. The development of Skyline grew into an entire ecosystem of tools and has since expanded beyond targeted proteomics. The Skyline software ecosystem is one of the most widely used software platforms in all of mass spectrometry.

The current software and its thriving community create exciting new opportunities for quantitative mass spectrometry. As of June 2020, Skyline has been installed over 110,000 times, has over 14,000 registered users on its website (http://skyline.ms), and is booted up over 9,000 times per week (exceeding 17,500 bootups in a single week).

The Skyline project has grown beyond the bounds of a single tool. There are now 16 Skyline external tools that rely on a formalized framework in Skyline, with more in development. Some of these tools have been installed over 10,000 times. We have also created the Panorama Knowledgebase (http://panoramaweb.org) and Panorama Public, a platform where Skyline users can organize, share, and disseminate processed quantitative proteomics data. Furthermore, our lab is now the primary contributor to Chorus (http://chorusproject.org), a unique mass spectrometry file sharing resource.

In this grant, we propose creating a resource that will enable the continued development and maintenance of these community tools and their dissemination within the community. These tools support over 14,000 registered users in their basic science, pre-clinical, and translational research.

Specifically, our proposal has four aims:

1) Expand our test infrastructure to improve the robustness, stress test the software, confirm compatibility across computer systems, and track performance over time.

2) Improve support for both proteomics and non-proteomics workflows.

3) Improve the collection, sharing, annotation, and dissemination of mass spectrometry data and Skyline documents.

4) Provide continued support and training for the Skyline ecosystem.

University Of Washington

THE NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES (NIGMS) SUPPORTS BASIC RESEARCH THAT INCREASES OUR UNDERSTANDING OF BIOLOGICAL PROCESSES AND LAYS THE FOUNDATION FOR ADVANCES IN DISEASE DIAGNOSIS, TREATMENT, AND PREVENTION. NIGMS ALSO SUPPORTS RESEARCH IN SPECIFIC CLINICAL AREAS THAT AFFECT MULTIPLE ORGAN SYSTEMS: ANESTHESIOLOGY AND PERI-OPERATIVE PAIN, CLINICAL PHARMACOLOGY ?COMMON TO MULTIPLE DRUGS AND TREATMENTS, AND INJURY, CRITICAL ILLNESS, SEPSIS, AND WOUND HEALING.? NIGMS-FUNDED SCIENTISTS INVESTIGATE HOW LIVING SYSTEMS WORK AT A RANGE OF LEVELSFROM MOLECULES AND CELLS TO TISSUES AND ORGANSIN RESEARCH ORGANISMS, HUMANS, AND POPULATIONS. ADDITIONALLY, TO ENSURE THE VITALITY AND CONTINUED PRODUCTIVITY OF THE RESEARCH ENTERPRISE, NIGMS PROVIDES LEADERSHIP IN SUPPORTING THE TRAINING OF THE NEXT GENERATION OF SCIENTISTS, ENHANCING THE DIVERSITY OF THE SCIENTIFIC WORKFORCE, AND DEVELOPING RESEARCH CAPACITY THROUGHOUT THE COUNTRY.

93.859 - Biomedical Research and Research Training

National Institute of General Medical Sciences (NIGMS) [HHS - NIH]

Seattle, Washington 981951016 United States

Single Zip Code

Limited Competition: NIGMS National and Regional Resources (R24 - Clinical Trial Not Allowed) (PAR-19-301)

Amendment Since initial award the total obligations have increased 400% from $1,113,806 to $5,569,030.