Bruker Announces New Quantitative Proteomics Capabilities with Skyline Software

At the 11th HUPO Annual World Congress the MacCoss lab of Biological Mass Spectrometry, at the University of Washington in Seattle, introduced a new version of Skyline Software, now supporting the Bruker maXis™ series of ultra-high resolution ESI-Qq-TOF mass spectrometers.

Skyline is a widely used, open source proteomics software platform for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM) and Full-Scan (MS1 and MS/MS) quantitative methods and analyzing the resulting data. It employs cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies.

Recently, Skyline developers have added support for a variety of full-scan chromatography-based quantitative proteomics approaches for QTOF and ion trap instruments. These include: MS1 filtering, targeted MS/MS and data independent acquisition (DIA). This fall, the release of a version of Skyline is planned that will add full support of Bruker ESI-Qq-TOF instruments.

Combining Skyline software with Bruker's recently introduced complete proteomics solution comprised of the nanoAdvance™ UHPLC, the unique CaptiveSpray™ ion source and Ultra-High-Resolution UHR-TOF maXis™ impact will add new quantitative capabilities to Bruker's fully integrated proteomics solution. More detailed information about qualitative and quantitative proteomics on maXis impact and quantitative data analyses by Skyline will be presented at the Bruker users' meeting at the HUPO conference on Monday September 10th.

Brendan MacLean, Software Project Manager for Skyline at the University of Washington School of Medicine, Department of Genome Sciences, said: "The Bruker team has been great to work with. They have clearly made Skyline integration with their instruments a high priority, and the resulting level of interaction and progress in this joint effort is impressive."

Dr. Michael MacCoss, Professor at the University of Washington, School of Medicine, Department of Genome Sciences, said: "We are really excited to support the analysis of Bruker mass spectrometry data. We have always wanted Skyline to support all LC-MS data and we are thankful for the opportunity to expand our analysis capabilities to include Bruker instrumentation."

Dr. Alexander Harder, Director of Product Management at Bruker Daltonics, commented: "We are very pleased to enable our customers to work with Skyline. Brendan has created a team of very talented developers and with more than 12,500 installations of Skyline. The MacCoss lab has set the gold standard for targeted proteomics. This nicely complements our instruments and bioinformatics platform for proteomics applications."