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Enhanced separation performance with reduced carry-over for proteomics analyses using novel nanoLC and the timsTOF HT

Industry - Full Day Session Other

Abstract #325 Posted on28 March 202524 April 2025 24 April 2025 14h41

Author(s)

Ines Metatla | Necker Proteomics Platform | 160 rue de Vaugirard, 75015, Paris, France
Chiara Guerrera | Necker Proteomics Platform | 160 rue de Vaugirard, 75015, Paris, France
Cerina Chhuon | Necker Proteomics Platform | 160 rue de Vaugirard, 75015, Paris, France
Petra Martinovic | Bruker Daltonik GmbH & Co KG | Fahrenheitstrasse 4, 28359, Bremen, Germany
Mario Mirabelli | Bruker Switzerland AG | IndustrieStrasse 26, 8117, Fällanden, Switzerland
Pierre-Olivier Schmit | Bruker France SAS | 34, rue de l'industrie, 67160, Wissembourg, France
Sabine Jourdain (Presenting Author) | Bruker France SAS | 34, rue de l'industrie, 67160, Wissembourg, France
Helena Alamil | Bruker France SAS | 34, rue de l'industrie, 67160, Wissembourg, France
Benoit Fatou | Bruker France SAS | 34, rue de l'industrie, 67160, Wissembourg, France
Manuel Chapelle | Bruker France SAS | 34, rue de l'industrie, 67160, Wissembourg, France
Goran Mitulović | Bruker Switzerland AG | IndustrieStrasse 26, 8117, Fällanden, Switzerland

Abstract

The development of modern mass spectrometry instrumentation led to an increase of peptide and protein identifications and better quantitation. However, even with the latest separation technologies, innovative stationary phases and instrumentation, analytes originating from a previously injected sample are detectable in the subsequent run. This is a significant problem causing delays and issues with quantitative and qualitative analysis.
Here, we use a novel nanoLC system with an increased sample loading speed and advanced wash of the injection path to reduce the carryover in proteomics analyses. Thus, the sample throughput increases and redundant cleaning steps are reduced.
All separations were performed using an innovative nanoLC separation system with a dedicated and tunable wash procedure of the injection path. Sample analysis was performed using direct sample injection on the separation and trap columns. HeLa cell line tryptic digests were injected directly onto a C18 separation column (PepSep Ultra) or a 5mm trap column. The nanoLC was coupled to a TimsTOF HT (Bruker Daltonics) mass spectrometer. All acquisitions were performed using a dia-PASEF acquisition method, and data were analyzed using DIA-NN in library-free mode.
The analysis of a complex cell lysate yielded 7835 ±84 protein IDs and a 6% carryover upon applying the wash procedure.

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