« Back
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
Poster Views: 1,502
View poster »

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 »
Ask the author a question about this poster.
Ask a Question »

Creative Commons

Related Posters

Creative Proteomics: Bioinformatics Analysis Network Analysis
Creative Proteomics

Creative Proteomics: Protein post-translational modification analysis
Creative Proteomics

Creative Proteomics: Flow Cytometry vs Microscopy
Creative Proteomics

CCS-centric protein identification using IM Score
Robin Park1, Patrick Garrett3, Sven Brehmer2, Titus Jung3, Vijayaraja Gnanasambandan1, Marc-Antoine Beauvais1, Sebastian Wehner2, Lennard Pfennig2, Hyunsoo Kim3, Christopher Adams1, Dennis Trede2, John R. Yates, III3, Rohan Thakur1 1Bruker Daltonics Inc., USA 2Bruker Daltonik GmbH, Bremen, Germany 3Scripps Research, San Diego, USA

Real-time search of Ubiquitin diGLY modified peptides and PaSER acquisition control on the timsTOF PRO
Christopher Adams1; Robin Park1; Nagarjuna Nagaraj4; Sven Brehmer4; Matt Willetts3; Elizabeth Gordon3; Barry M. Zee2; Hayley Peckham2; Kimberly Lee2; Tharan Srikumar3 1Bruker,San Jose,CA;2Cell Signaling Technologies, Danvers, MA;3Bruker, Billerica, MA; 4Bruker, Bremen, Germany