Category: Panorama Partners Program

08 Jun 2016

Skyline User Group Presentation: Improved Quality Control Workflows and Other Panorama Updates

06082016-josh-asms-video-presentationDidn’t make it to this year’s Skyline User Group Meeting? Watch recorded sessions from the event, including Josh Eckels presentation on “Improved Quality Control Workflows and Other Panorama Updates.”

Watch Presentation

 

Presentation Overview

Panorama is a web-based complement to Skyline, used by more than a hundred organizations to manage, analyze, and share targeted mass spec data generated by Skyline. Since being unveiled at ASMS 2015, Panorama’s support for QC workflows has expanded significantly. With input from the SProCoP team and the user community, new and improved metrics, automation, and visualizations build on the previous functionality. Additionally, Skyline and Panorama now include document version tracking for method building and other workflows, and Panorama now supports small molecule data. This presentation will demonstrate the new capabilities and outline plans for Panorama’s ongoing development.

About Josh

Josh Eckels has lead development on proteomics related projects for LabKey Server over the past 10+ years, and he currently oversees Panorama development. He is experienced in security-related projects, client-side end user applications, and server-side development. Prior to joining LabKey, Josh worked most recently on Amazon.com’s data warehouse, developing the software that schedules and executes loading and querying of more than 30 terabytes of data. Before that, he was the team lead for the debugger for BEA System’s WebLogic Workshop. At LabKey, he focuses on mass spectrometry, other assay types, experimental annotations and general infrastructure. Josh has a BS in Computer Engineering from Northwestern University.

03 Jun 2016

LabKey @ ASMS 2016

Heading to ASMS 2016? Join LabKey Vice President Josh Eckels for the latest updates on Panorama presented at sessions throughout the week (schedule below) or stop by the Agilent hospitality suite Monday – Wednesday to learn more about Panorama.

Skyline User Group Meeting Presentation: Improved Quality Control Workflows and Other Panorama Updates

Sunday, June 5
Sheraton Gunter, 205 E. Houston St., San Antonio, TX

Introduction: Panorama is a web-based complement to Skyline, used by more than a hundred organizations to manage, analyze, and share targeted mass spec data generated by Skyline. Since being unveiled at ASMS 2015, Panorama’s support for QC workflows has expanded significantly. With input from the SProCoP team and the user community, new and improved metrics, automation, and visualizations build on the previous functionality. Additionally, Skyline and Panorama now include document version tracking for method building and other workflows, and Panorama now supports small molecule data. This presentation will demonstrate the new capabilities and outline plans for Panorama’s ongoing development.

Monday Workshop 14: Tracking through Statistical QC Monitoring (LC/MS & Related Topics Interest Group)

Monday, June 6 | 5:45 -7:00PM
Room 305, level 3

About the Session: Liquid chromatography mass spectrometry systems are recognized as highly sensitive and specific tools for metabolomic and proteomic analyses. Ensuring the integrity of data through a system of controls referred to as quality control standards enables a higher level of confidence in the obtained results. Providing intra-laboratory personnel with quality control charts allows for correction when standards exceed acceptability limits. Control charts may be used in an inter-laboratory manner to compare results across labs. By monitoring performance standards, a higher level of commutability of experimental results may be achieved.

The workshop will provide a demonstration of online QC tracking through Skyline; system performance tracking and control charting. The workshop will explore available controls for tryptic digestion to ensure proteolytic cleavage. The content will also include a section related to metabolomic analyses.

Integrating quality control and performance standards in the experimental design is not a new concept. However, the intention to monitor these standards over time and across experiments presents an opportunity. A major limitation in the broader analysis of experimental control performance has been aggregation and visualization. Precious samples may be better utilized by identifying a trend and performing a preventive action to avoid a failed assay. The overall aim is to shift to a prospective action driven review rather than a retrospective control review approach.

Poster: Managing Small Molecule Targeted Mass Spec Assays using Skyline and Panorama

Thursday, June 9 | 10:30AM – 2:30PM
Poster Number: (ThP 269)

Introduction: Panorama’s new support for small molecule assays extends the features previously available for managing proteomics assays, including automated quality control workflows, data management and visualization, and secure sharing with internal and external collaborators. The popular Skyline targeted mass spec desktop application added support for small molecule assays in 2015, and this recent work closely integrates Panorama, bringing its newly improved support for monitoring multiple mass spec instruments’ performance at a glance. Additionally, Panorama adds capabilities to track revisions of the Skyline document for method building and similar uses. Developed as a module in the LabKey Server data management platform, Panorama is freely available, open source and may be installed and managed by any laboratory or organization.  Free, hosted Panorama projects are also available on panoramaweb.org.

19 Mar 2016

Brendan MacLean Awarded 2016 Gilbert S. Omenn Computational Proteomics Award

Brendan MacLean, 2016 Gilbert S. Omenn Computational Proteomics Award RecipientCongratulations to Brendan MacLean of University of Washington’s MacCoss Lab for being awarded the 2016 Gilbert S. Omenn Computational Proteomics Award!

Brendan is one of the founding partners of LabKey and was a key programmer in the development of the Computational Proteomics Analysis System (CPAS) which would eventually become LabKey Server. He also made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline. Since August, 2008 he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community.

The Gilbert S. Omenn Computational Proteomics Award is awarded by US HUPO to recognize the specific achievements of scientists that have developed software tools used by the proteomics community. The importance of and reliance on computational software is sometimes under-recognized. This award is named in honor of Gil Omenn, a US HUPO Past President, leader of the Human Proteome Project, and influential proteomics researcher.

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