Monday, December 2, 2013

Boost your analysis speed with PEAKS 7

New mass spectrometry instruments come out every year with higher resolution and/or scan rate. This causes an increasing amount of data generated per hour. While the accuracy and sensitivity of the software tools are critical, many researchers have the need to complete the analysis sooner without compromising the accuracy or sensitivity.

In PEAKS 7, we have re-engineered many parts of the algorithms to make them more efficient.
"The increase in speed [of PEAKS 7] is quite remarkable."
Paul Taylor, Sick Kids Hospital
In this post, we will use an internal test to illustrate the dramatic speed improvements our users love.

Test data and search parameters

12 files generated from Thermo Q-Exactive instrument was used. Both MS and MS/MS were acquired on high resolution. In total, there are more than 100,000 MS/MS spectrum. The detail search parameters is as follow.


Test hardware and operating system

Mac mini late 2012 version. Intel i7-3720QM processor at 2.6GHz. 16GB RAM. Windows 7 Professional Edition 64 bit. The Windows OS is installed using Boot Camp.

The test and the result

PEAKS 6 and PEAKS 7 were installed on the same Mac mini computer. The computer was rebooted between analysis.

First off, we want to test our much loved de novo sequencing speed improvement and here is the result. PEAKS 7 de novo is more than five time faster!
The complete analysis in PEAKS can identify database peptides, novel peptides, PTMs and mutated peptides in one go. We use the total running time in version 6 as the baseline and see how much shorter researchers can finish the same analysis.
The same search completed in just one quarter of what it takes in the previous version, with the same level of accuracy and sensitivity.