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PEAKS™ Software for the processing of timsTOF Pro PASEF data: identification and label-free quantitation
Poster Title: PEAKS™ Software for the processing of timsTOF Pro PASEF data: identification and label-free quantitation
Submitted on 11 Apr 2019
Author(s): Markus Lubeck(1), Heiner Koch(1), Scarlet Beck(1), Paul Savage(2), Oliver Raether(1), Pierre-Olivier Schmit(2) Paul Shan (3) and Gary Kruppa (4)
Affiliations: (1) Bruker Daltoniks GmbH, Bremen-Germany, (2) Bruker France SA, Wissembourg, France, (3) Bioinformatics Solutions, Waterloo, Canada, (4) Bruker Daltonics Inc, Billerica, USA
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Poster Information
Abstract: The performance of a timsTOFPro instrument with PASEF for shotgun proteomics (Bruker Daltonics) has been evaluated using tryptic digests of human cancer cell lysates (HeLa) (Pierce) and mouse heart cell digests. Chromatographic separations were performed on a nanoElute (Bruker) nano-UHPLC using a 25 cm, 75 μm ID Odyssey C18 nanocolumn with integrated emitter (IonOpticks, Australia) at 400 nl/min and column oven at 50 °C with direct loading. Data was analyzed using multiple interations of the PEAKS ( and Perseus (Jürgen Cox, Max Planck Institute of Biochemistry) software. Results were normalized to <1% FDR on PSMs.

Summary: Here we describe how a modified version of the well-known PEAKS™ proteomics processing software suite can be used for the processing of PASEF datasets.Report abuse »
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