ArticleJournal of proteome research2021
Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Analysis of FAIMS for the study of affinity-purified protein complexes using the orbitrap ascend tribrid mass spectrometer.Molecular omics · 2025Article
- Multi-omics analysis to uncover the molecular basis of tumor budding in head and neck squamous cell carcinoma.NPJ precision oncology · 2025Article
- Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics.Nature biotechnology · 2025Article
- Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Matched Tissues for Proteomics and Phosphoproteomics.ACS omega · 2025Article
- Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study.The EMBO journal · 2025Article
- Robust, Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme.Journal of proteome research · 2024Article
- A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A region-resolved proteomic map of the human brain enabled by high-throughput proteomics.The EMBO journal · 2023Article
- Article
- High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing.Journal of proteome research · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
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.
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