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Eckert S, Chang YC, Bayer FP, The M, Kuhn PH, Weichert W, Kuster B. Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue. J Proteome Res 2021; 20:5402-5411. [PMID: 34735149 DOI: 10.1021/acs.jproteome.1c00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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Affiliation(s)
- Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising 85354, Germany
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Yan T, Desai HS, Boatner LM, Yen SL, Cao J, Palafox MF, Jami-Alahmadi Y, Backus KM. SP3-FAIMS Chemoproteomics for High-Coverage Profiling of the Human Cysteinome*. Chembiochem 2021; 22:1841-1851. [PMID: 33442901 DOI: 10.1002/cbic.202000870] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/12/2021] [Indexed: 12/23/2022]
Abstract
Chemoproteomics has enabled the rapid and proteome-wide discovery of functional, redox-sensitive, and ligandable cysteine residues. Despite widespread adoption and considerable advances in both sample-preparation workflows and MS instrumentation, chemoproteomics experiments still typically only identify a small fraction of all cysteines encoded by the human genome. Here, we develop an optimized sample-preparation workflow that combines enhanced peptide labeling with single-pot, solid-phase-enhanced sample-preparation (SP3) to improve the recovery of biotinylated peptides, even from small sample sizes. By combining this improved workflow with on-line high-field asymmetric waveform ion mobility spectrometry (FAIMS) separation of labeled peptides, we achieve unprecedented coverage of >14000 unique cysteines in a single-shot 70 min experiment. Showcasing the wide utility of the SP3-FAIMS chemoproteomic method, we find that it is also compatible with competitive small-molecule screening by isotopic tandem orthogonal proteolysis-activity-based protein profiling (isoTOP-ABPP). In aggregate, our analysis of 18 samples from seven cell lines identified 34225 unique cysteines using only ∼28 h of instrument time. The comprehensive spectral library and improved coverage provided by the SP3-FAIMS chemoproteomics method will provide the technical foundation for future studies aimed at deciphering the functions and druggability of the human cysteineome.
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Affiliation(s)
- Tianyang Yan
- Department of Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Department of Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Lisa M Boatner
- Department of Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Stephanie L Yen
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Jian Cao
- Department of Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Maria F Palafox
- Department of Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.,Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Keriann M Backus
- Department of Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.,DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA.,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
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Bonneil E, Pfammatter S, Thibault P. Enhancement of mass spectrometry performance for proteomic analyses using high-field asymmetric waveform ion mobility spectrometry (FAIMS). J Mass Spectrom 2015; 50:1181-1195. [PMID: 26505763 DOI: 10.1002/jms.3646] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 06/05/2023]
Abstract
Remarkable advances in mass spectrometry sensitivity and resolution have been accomplished over the past two decades to enhance the depth and coverage of proteome analyses. As these technological developments expanded the detection capability of mass spectrometers, they also revealed an increasing complexity of low abundance peptides, solvent clusters and sample contaminants that can confound protein identification. Separation techniques that are complementary and can be used in combination with liquid chromatography are often sought to improve mass spectrometry sensitivity for proteomics applications. In this context, high-field asymmetric waveform ion mobility spectrometry (FAIMS), a form of ion mobility that exploits ion separation at low and high electric fields, has shown significant advantages by focusing and separating multiply charged peptide ions from singly charged interferences. This paper examines the analytical benefits of FAIMS in proteomics to separate co-eluting peptide isomers and to enhance peptide detection and quantitative measurements of protein digests via native peptides (label-free) or isotopically labeled peptides from metabolic labeling or chemical tagging experiments.
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Affiliation(s)
- Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Sibylle Pfammatter
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
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