Evaluation of Disposable Trap Column nanoLC−FAIMS−MS/MS for the Proteomic Analysis of FFPE Tissue
2021-11-04
Stephan Eckert, Yun-Chien Chang, Florian P. Bayer, Matthew The, Peer-Hendrik Kuhn, Wilko Weichert, Bernhard Kuster
J-Proteomw Res., 20, 5402 − 5411, 2023
Proteomic biomarker discovery using formalin-fixed paraffin-embedded (FFPE) tissue requires robust workflows to support the analysis of large cohorts of patient samples. It also requires finding a
reasonable balance between achieving a high proteomic depth and limiting the overall analysis time. To this end, we evaluated the merits of online coupling of single-use disposable trap column nanoflow liquid chromatography, high-field asymmetric-waveform ion-mobility spectrometry (FAIMS), and tandem mass spectrometry (nLC−FAIMS−MS/MS). The data show that ≤600 ng of peptide digest should be loaded onto the chromatographic part of the system. Careful characterization of the FAIMS settings enabled the choice of optimal combinations of compensation voltages (CVs) as a function of the employed LC gradient time. We found nLC−FAIMS−MS/MS to be on par with StageTip-based off-line basic pH reversed-phase fractionation in terms of proteomic depth and reproducibility of protein quantification (coefficient of variation ≤15% for 90% of all proteins) but requiring 50% less sample and substantially reducing sample handling. Using FFPE materials from the lymph node, lung, and prostate tissue as examples, we show that nLC−FAIMS−MS/MS can identify 5000−6000 proteins from the respective tissue within a total of 3 h of analysis time. KEYWORDS: quantitative proteomics, clinical proteomics, FFPE analysis, high-field asymmetric waveform ion mobility spectrometry (FAIMS), LC−FAIMS−MS/MS
Speaker: Prof. Dr. Thomas Carell
Ludwig-Maximilians-Universität München
Institut für Chemische Epigenetik (ICEM)
Department of Chemistry
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Institute for Chemical Epigenetics Munich (ICEM)
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Institute for Chemical Epigenetics Munich (ICEM)
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LMU Munich
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LMU Munich
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LMU Munich
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