Thermo Fisher Scientific Introduces Instrument Control Software for its Hybrid Mass Spectrometer That Enables Data-Independent Acquisition for Proteomics
New Control Software on Thermo Scientific Q Exactive MS Enables DIA and Targeted Quantitation on Same Instrument
The next generation of high-throughput quantitative proteomics is imminent


Monday, September 10, 2012 7:59 am EDT

BOSTON – HUPO 11th Annual World Congress -- (Sept. 10, 2012) – Thermo Fisher Scientific Inc., the world leader in serving science, today introduced a new data-independent acquisition (DIA) proteomics capability  for the Thermo Scientific Q Exactive high performance quadrupole-Orbitrap LC-MS/MS. The new DIA feature allows the Q ExactiveTM mass spectrometer to collect MS/MS spectra on virtually all ions in a sample by selecting broad m/z windows and fragmenting all precursors in that window. This allows the instrument to quantify nearly all detected peptides in the sample in a single run.

Unlike other DIA-capable mass spectrometry platforms, which require switching to a triple quadrupole instrument to perform targeted peptide quantitation, Q Exactive LC/MS now lets users perform both DIA and targeted quantification experiments on the same instrument.

The DIA data collected on the Q Exactive MS can be processed with Thermo Scientific Pinpoint software 1.3. The DIA acquisition strategy adds another multiplexing method to the Q Exactive instrument, which already allows users to multiplex up to 10 precursor ions for quantification in full MS and MS/MS mode.

The Q Exactive MS offers ultrahigh resolution up to 140,000 This delivers very accurate quantitation by decreasing interference from targeted peptidesThis makes the technique especially useful for quantifying proteins/peptides of interest from DIA experiments. Plus, the Q Exactive instrument provides truly SRM-equivalent quantitative performance.

“The next generation of high-throughput quantitative proteomics is imminent,” said Andreas Huhmer, marketing director, Thermo Fisher. “Multiplexing strategies, such as the data-independent acquisition methods, will play an important role in elevating quantitative proteomics to this new level, and the unique architecture of hybrid Orbitrap instruments will play an important role in advancing the technique.”

The new instrument control software is available as a developer’s kit for Q Exactive LC/MS customers who want to acquire DIA capability.

The Q Exactive instrument is the first commercially available mass spectrometer to combine quadrupole precursor selection with HR/AM Orbitrap mass analysis to deliver high confidence quantitative/qualitative workflows. Thermo Fisher coined the term “Quanfirmation” to describe the instrument’s ability to perform compound identification, quantitation and confirmation in a single run.

For more information about the new DIA capability for the Q Exactive LC/MS, please visit, call 1-800-532-4752 or email

About Thermo Fisher Scientific

Thermo Fisher Scientific Inc. is the world leader in serving science. Our mission is to enable our customers to make the world healthier, cleaner and safer. With revenues of $12 billion, we have approximately 39,000 employees and serve customers within pharmaceutical and biotech companies, hospitals and clinical diagnostic labs, universities, research institutions and government agencies, as well as in environmental and process control industries. We create value for our key stakeholders through three premier brands, Thermo Scientific, Fisher Scientific and Unity™ Lab Services, which offer a unique combination of innovative technologies, convenient purchasing options and a single solution for laboratory operations management. Our products and services help our customers solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity. Visit




Stu Matlow
1 (408) 965-6408