Tuesday, July 16, 2013

PEAKS performs excellently on AB SCIEX TripleTOF 5600 data

AB SCIEX TripleTOF 5600 is a powerful instrument that provides high mass accuracy and high resolution in both MS and MS/MS modes. With the ability to acquire a maximum of 50 MS/MS spectra per second, the instrument makes a great component for a proteomics research platform.

PEAKS algorithm has been optimized specifically for this type of instrument in version 6. A comparative study was performed using iPRG 2012 dataset against Mascot and ProteinPilot. The results are shown in the following table.


At 1% FDR, PEAKS 6 was able to identify twice as many PSMs as the popularly used Mascot + Percolator combination. Even compared with AB SCIEX’s ProteinPilot software, PEAKS 6 identified 29% more PSMs.


*The content of this post is extracted from ASMS 2012 poster "Optimized Database Search Software for Peptide Identification with AB SCIEX TripleTOF 5600". You can find a copy of the poster here.

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