1
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Greguš M, Koller A, Ray S, Ivanov AR. Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples. J Proteome Res 2024; 23:2230-2240. [PMID: 38690845 PMCID: PMC11165581 DOI: 10.1021/acs.jproteome.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Deep proteomic profiling of complex biological and medical samples available at low nanogram and subnanogram levels is still challenging. Thorough optimization of settings, parameters, and conditions in nanoflow liquid chromatography-tandem mass spectrometry (MS)-based proteomic profiling is crucial for generating informative data using amount-limited samples. This study demonstrates that by adjusting selected instrument parameters, e.g., ion injection time, automated gain control, and minimally altering the conditions for resuspending or storing the sample in solvents of different compositions, up to 15-fold more thorough proteomic profiling can be achieved compared to conventionally used settings. More specifically, the analysis of 1 ng of the HeLa protein digest standard by Q Exactive HF-X Hybrid Quadrupole-Orbitrap and Orbitrap Fusion Lumos Tribrid mass spectrometers yielded an increase from 1758 to 5477 (3-fold) and 281 to 4276 (15-fold) peptides, respectively, demonstrating that higher protein identification results can be obtained using the optimized methods. While the instruments applied in this study do not belong to the latest generation of mass spectrometers, they are broadly used worldwide, which makes the guidelines for improving performance desirable to a wide range of proteomics practitioners.
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Affiliation(s)
- Michal Greguš
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Antonius Koller
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Somak Ray
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Alexander R. Ivanov
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
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2
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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3
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Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Mol Syst Biol 2024; 20:458-474. [PMID: 38454145 PMCID: PMC10987601 DOI: 10.1038/s44320-024-00025-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.
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Affiliation(s)
- Mira L Burtscher
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | | | | | - Katharina Zirngibl
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.
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4
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Steigerwald S, Sinha A, Fort KL, Zeng WF, Niu L, Wichmann C, Kreutzmann A, Mourad D, Aizikov K, Grinfeld D, Makarov A, Mann M, Meier F. Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis. Mol Cell Proteomics 2024; 23:100713. [PMID: 38184013 PMCID: PMC10851225 DOI: 10.1016/j.mcpro.2024.100713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024] Open
Abstract
Optimizing data-independent acquisition methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here, we describe a real-time full mass range implementation of the phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2 h analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here, the number of identified protein groups and peptides increased by >15% in comparison to enhanced Fourier transformation processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.
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Affiliation(s)
- Sophia Steigerwald
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kyle L Fort
- Thermo Fisher Scientific (GmbH), Bremen, Germany
| | - Wen-Feng Zeng
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lili Niu
- Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christoph Wichmann
- Department Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | | | - Matthias Mann
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Florian Meier
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Functional Proteomics, Jena University Hospital, Jena, Germany.
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5
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He Y, Shishkova E, Peters-Clarke TM, Brademan DR, Westphall MS, Bergen D, Huang J, Huguet R, Senko MW, Zabrouskov V, McAlister GC, Coon JJ. Evaluation of the Orbitrap Ascend Tribrid Mass Spectrometer for Shotgun Proteomics. Anal Chem 2023; 95:10655-10663. [PMID: 37389810 PMCID: PMC10528367 DOI: 10.1021/acs.analchem.3c01155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a powerful technology to globally profile protein abundances, activities, interactions, and modifications. The extreme complexity of proteomics samples, which often contain hundreds of thousands of analytes, necessitates continuous development of MS techniques and instrumentation to improve speed, sensitivity, precision, and accuracy, among other analytical characteristics. Here, we systematically evaluated the Orbitrap Ascend Tribrid mass spectrometer in the context of shotgun proteomics, and we compared its performance to that of the previous generation of Tribrid instruments─the Orbitrap Eclipse. The updated architecture of the Orbitrap Ascend includes a second ion-routing multipole (IRM) in front of the redesigned C-trap/Orbitrap and a new ion funnel that allows gentler ion introduction, among other changes. These modifications in Ascend hardware configuration enabled an increase in parallelizable ion injection time during higher-energy collisional dissociation (HCD) Orbitrap tandem MS (FTMS2) analysis of ∼5 ms. This enhancement was particularly valuable in the analyses of limited sample amounts, where improvements in sensitivity resulted in up to 140% increase in the number of identified tryptic peptides. Further, analysis of phosphorylated peptides enriched from the K562 human cell line yielded up to ∼50% increase in the number of unique phosphopeptides and localized phosphosites. Strikingly, we also observed a ∼2-fold boost in the number of detected N-glycopeptides, likely owing to the improvements in ion transmission and sensitivity. In addition, we performed the multiplexed quantitative proteomics analyses of TMT11-plex labeled HEK293T tryptic peptides and observed 9-14% increase in the number of quantified peptides. In conclusion, the Orbitrap Ascend consistently outperformed its predecessor the Orbitrap Eclipse in various bottom-up proteomic analyses, and we anticipate that it will generate reproducible and in-depth datasets for numerous proteomic applications.
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Affiliation(s)
- Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | | | | | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - David Bergen
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | | | | | | | | | | | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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6
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Alvarez-Rivera E, Ortiz-Hernández EJ, Lugo E, Lozada-Reyes LM, Boukli NM. Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms. Proteomes 2023; 11:22. [PMID: 37489388 PMCID: PMC10366845 DOI: 10.3390/proteomes11030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/26/2023] Open
Abstract
Recent advances in the field of proteomics have allowed extensive insights into the molecular regulations of the cell proteome. Specifically, this allows researchers to dissect a multitude of signaling arrays while targeting for the discovery of novel protein signatures. These approaches based on data mining are becoming increasingly powerful for identifying both potential disease mechanisms as well as indicators for disease progression and overall survival predictive and prognostic molecular markers for cancer. Furthermore, mass spectrometry (MS) integrations satisfy the ongoing demand for in-depth biomarker validation. For the purpose of this review, we will highlight the current developments based on MS sensitivity, to place quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data for future applications in cancer precision medicine. We will also discuss malignancies associated with oncogenic viruses such as Acquire Immunodeficiency Syndrome (AIDS) and suggest novel mechanisms behind this phenomenon. Human Immunodeficiency Virus type-1 (HIV-1) proteins are known to be oncogenic per se, to induce oxidative and endoplasmic reticulum stresses, and to be released from the infected or expressing cells. HIV-1 proteins can act alone or in collaboration with other known oncoproteins, which cause the bulk of malignancies in people living with HIV-1 on ART.
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Affiliation(s)
- Eduardo Alvarez-Rivera
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Emanuel J. Ortiz-Hernández
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Elyette Lugo
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | | | - Nawal M. Boukli
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
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7
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Matzinger M, Mayer RL, Mechtler K. Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing. Proteomics 2023; 23:e2200162. [PMID: 36806919 PMCID: PMC10909491 DOI: 10.1002/pmic.202200162] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/21/2023]
Abstract
The ability to map a proteomic fingerprint to transcriptomic data would master the understanding of how gene expression translates into actual phenotype. In contrast to nucleic acid sequencing, in vitro protein amplification is impossible and no single cell proteomic workflow has been established as gold standard yet. Advances in microfluidic sample preparation, multi-dimensional sample separation, sophisticated data acquisition strategies, and intelligent data analysis algorithms have resulted in major improvements to successfully analyze such tiny sample amounts with steadily boosted performance. However, among the broad variation of published approaches, it is commonly accepted that highest possible sensitivity, robustness, and throughput are still the most urgent needs for the field. While many labs have focused on multiplexing to achieve these goals, label-free SCP is a highly promising strategy as well whenever high dynamic range and unbiased accurate quantification are needed. We here focus on recent advances in label-free single-cell mass spectrometry workflows and try to guide our readers to choose the best method or combinations of methods for their specific applications. We further highlight which techniques are most propitious in the future and which applications but also limitations we foresee for the field.
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Affiliation(s)
- Manuel Matzinger
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
| | - Rupert L. Mayer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
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8
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Phaneuf CG, Aizikov K, Grinfeld D, Kreutzmann A, Mourad D, Lange O, Dai D, Zhang B, Belenky A, Makarov AA, Ivanov AR. Experimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays. Commun Chem 2023; 6:64. [PMID: 37024568 PMCID: PMC10079678 DOI: 10.1038/s42004-023-00861-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Mass spectrometry (MS)-based thermal stability assays have recently emerged as one of the most promising solutions for the identification of protein-ligand interactions. Here, we have investigated eight combinations of several recently introduced MS-based advancements, including the Phase-Constrained Spectral Deconvolution Method, Field Asymmetric Ion Mobility Spectrometry, and the implementation of a carrier sample as improved MS-based acquisition approaches for thermal stability assays (iMAATSA). We used intact Jurkat cells treated with a commercially available MEK inhibitor, followed by heat treatment, to prepare a set of unfractionated isobarically-labeled proof-of-concept samples to compare the performance of eight different iMAATSAs. Finally, the best-performing iMAATSA was compared to a conventional approach and evaluated in a fractionation experiment. Improvements of up to 82% and 86% were demonstrated in protein identifications and high-quality melting curves, respectively, over the conventional approach in the proof-of-concept study, while an approximately 12% improvement in melting curve comparisons was achieved in the fractionation experiment.
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Affiliation(s)
- Clifford G Phaneuf
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | | | | | | | - Daniel Dai
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | - Bailin Zhang
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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9
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Matzinger M, Müller E, Dürnberger G, Pichler P, Mechtler K. Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics. Anal Chem 2023; 95:4435-4445. [PMID: 36802514 PMCID: PMC9996606 DOI: 10.1021/acs.analchem.2c05022] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The analysis of ultralow input samples or even individual cells is essential to answering a multitude of biomedical questions, but current proteomic workflows are limited in their sensitivity and reproducibility. Here, we report a comprehensive workflow that includes improved strategies for all steps, from cell lysis to data analysis. Thanks to convenient-to-handle 1 μL sample volume and standardized 384-well plates, the workflow is easy for even novice users to implement. At the same time, it can be performed semi-automatized using CellenONE, which allows for the highest reproducibility. To achieve high throughput, ultrashort gradient lengths down to 5 min were tested using advanced μ-pillar columns. Data-dependent acquisition (DDA), wide-window acquisition (WWA), data-independent acquisition (DIA), and commonly used advanced data analysis algorithms were benchmarked. Using DDA, 1790 proteins covering a dynamic range of four orders of magnitude were identified in a single cell. Using DIA, proteome coverage increased to more than 2200 proteins identified from single-cell level input in a 20 min active gradient. The workflow enabled differentiation of two cell lines, demonstrating its suitability to cellular heterogeneity determination.
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Affiliation(s)
- Manuel Matzinger
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Elisabeth Müller
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Gerhard Dürnberger
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Peter Pichler
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria.,Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
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10
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Zhang X, Sun H, Wang Z, Zhou S, Fu Y, Anthony HA, Peng J. In-Depth Blood Proteome Profiling by Extensive Fractionation and Multiplexed Quantitative Mass Spectrometry. Methods Mol Biol 2023; 2628:109-125. [PMID: 36781782 DOI: 10.1007/978-1-0716-2978-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Blood in the circulatory system carries information of physiological and pathological status of the human body, so blood proteins are often used as biomarkers for diagnosis, prognosis, and therapy. Human blood proteome can be explored by the latest technologies in mass spectrometry (MS), creating an opportunity of discovering new disease biomarkers. The extreme dynamic range of protein concentrations in blood, however, poses a challenge to detect proteins of low abundance, namely, tissue leakage proteins. Here, we describe a strategy to directly analyze undepleted blood samples by extensive liquid chromatography (LC) fractionation and 18-plex tandem-mass-tag (TMT) mass spectrometry. The proteins in blood specimens (e.g., plasma or serum) are isolated by acetone precipitation and digested into peptides. The resulting peptides are TMT-labeled, separated by basic pH reverse-phase (RP) LC into at least 40 fractions, and analyzed by acidic pH RPLC and high-resolution MS/MS, leading to the quantification of ~3000 unique proteins. Further increase of basic pH RPLC fractions and adjustment of the fraction concatenation strategy can enhance the proteomic coverage (up to ~5000 proteins). Finally, the combination of multiple batches of TMT experiments allows the profiling of hundreds of blood samples. This TMT-MS-based method provides a powerful platform for deep proteome profiling of human blood samples.
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Affiliation(s)
- Xue Zhang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - High A Anthony
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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11
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Steger M, Karayel Ö, Demichev V. Ubiquitinomics: history, methods and applications in basic research and drug discovery. Proteomics 2022; 22:e2200074. [PMID: 35353442 DOI: 10.1002/pmic.202200074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/08/2022]
Abstract
The ubiquitin-proteasome system (UPS) was discovered about 40 years ago and is known to regulate a multitude of cellular processes including protein homeostasis. ubiquitylated proteins are recognized by downstream effectors, resulting in alterations of protein abundance, activity, or localization. Not surprisingly, the ubiquitylation machinery is dysregulated in numerous diseases, including cancers and neurodegeneration. Mass spectrometry (MS)-based proteomics has emerged as a transformative technology for characterizing protein ubiquitylation in an unbiased fashion. Here, we provide an overview of the different MS-based approaches for studying protein ubiquitylation. We review various methods for enriching and quantifying ubiquitin modifications at the peptide or protein level, outline MS acquisition and data processing approaches and discuss key challenges. Finally, we examine how MS-based ubiquitinomics can aid both basic biology and drug discovery research. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Martin Steger
- Evotec München GmbH, Martinsried, 82152, Germany.,Present address: Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Özge Karayel
- Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Current address: Department of Physiological Chemistry, Genentech, South San Francisco, CA, 94080, USA
| | - Vadim Demichev
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
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12
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Ctortecka C, Stejskal K, Krššáková G, Mendjan S, Mechtler K. Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics. Anal Chem 2021; 94:2434-2443. [PMID: 34967612 PMCID: PMC8829824 DOI: 10.1021/acs.analchem.1c04174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Single-cell proteomics
workflows have considerably improved in
sensitivity and reproducibility to characterize as-yet unknown biological
phenomena. With the emergence of multiplexed single-cell proteomics,
studies increasingly present single-cell measurements in conjunction
with an abundant congruent carrier to improve the precursor selection
and enhance identifications. While these extreme carrier spikes are
often >100× more abundant than the investigated samples, the
total ion current undoubtably increases but the quantitative accuracy
possibly is affected. We here focus on narrowly titrated carrier spikes
(i.e., <20×) and assess their elimination for a comparable
sensitivity with superior accuracy. We find that subtle changes in
the carrier ratio can severely impact the measurement variability
and describe alternative multiplexing strategies to evaluate data
quality. Lastly, we demonstrate elevated replicate overlap while preserving
acquisition throughput at an improved quantitative accuracy with DIA-TMT
and discuss optimized experimental designs for multiplexed proteomics
of trace samples. This comprehensive benchmarking gives an overview
of currently available techniques and guides the conceptualization
of the optimal single-cell proteomics experiment.
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Affiliation(s)
- Claudia Ctortecka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Gabriela Krššáková
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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13
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Abstract
![]()
Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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14
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Pfammatter S, Wu Z, Bonneil E, Bailey DJ, Prasad S, Belford M, Rochon J, Picard P, Lacoursière J, Dunyach JJ, Thibault P. Integration of Segmented Ion Fractionation and Differential Ion Mobility on a Q-Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer. Anal Chem 2021; 93:9817-9825. [PMID: 34213903 DOI: 10.1021/acs.analchem.1c01376] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-field asymmetric waveform ion mobility spectrometry (FAIMS) has gained popularity in the proteomics field for its capability to improve mass spectrometry sensitivity and to decrease peptide co-fragmentation. The recent implementation of FAIMS on Tribrid Orbitrap instruments enhanced proteome coverage and increased the precision of quantitative measurements. However, the FAIMS interface has not been available on older generation Orbitrap mass spectrometers such as the Q-Exactive. Here, we report the integration of the FAIMS Pro device with embedded electrical and gas connections to a Q-Exactive HF mass spectrometer. Proteomic experiments performed on HeLa tryptic digests with the modified mass spectrometer improved signal to noise and reduced interfering ions, resulting in an increase of 42% in peptide identification. FAIMS was also combined with segmented ion fractionation where 100 m/z windows were obtained in turn to further increase the depth of proteome analysis by reducing the proportion of chimeric MS/MS spectra from 50 to 27%. We also demonstrate the application of FAIMS to improve quantitative measurements when using isobaric peptide labeling. FAIMS experiments performed on a two-proteome model revealed that FAIMS Pro provided a 65% improvement in quantification accuracy compared to conventional LC-MS/MS experiments.
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Affiliation(s)
- Sibylle Pfammatter
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Zhaoguan Wu
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Derek J Bailey
- ThermoFisher Scientific, San Jose, California 95134, United States
| | - Satendra Prasad
- ThermoFisher Scientific, San Jose, California 95134, United States
| | - Michael Belford
- ThermoFisher Scientific, San Jose, California 95134, United States
| | | | - Pierre Picard
- Phytronix Technologies, Québec, Quebec G1P 2J7, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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15
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Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M, Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T, Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function. Nat Commun 2021; 12:3962. [PMID: 34172723 PMCID: PMC8233319 DOI: 10.1038/s41467-021-23985-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/26/2021] [Indexed: 02/05/2023] Open
Abstract
Missense mutations in p53 are severely deleterious and occur in over 50% of all human cancers. The majority of these mutations are located in the inherently unstable DNA-binding domain (DBD), many of which destabilize the domain further and expose its aggregation-prone hydrophobic core, prompting self-assembly of mutant p53 into inactive cytosolic amyloid-like aggregates. Screening an oligopyridylamide library, previously shown to inhibit amyloid formation associated with Alzheimer's disease and type II diabetes, identified a tripyridylamide, ADH-6, that abrogates self-assembly of the aggregation-nucleating subdomain of mutant p53 DBD. Moreover, ADH-6 targets and dissociates mutant p53 aggregates in human cancer cells, which restores p53's transcriptional activity, leading to cell cycle arrest and apoptosis. Notably, ADH-6 treatment effectively shrinks xenografts harboring mutant p53, while exhibiting no toxicity to healthy tissue, thereby substantially prolonging survival. This study demonstrates the successful application of a bona fide small-molecule amyloid inhibitor as a potent anticancer agent.
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Affiliation(s)
- L Palanikumar
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Laura Karpauskaite
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mohamed Al-Sayegh
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Ibrahim Chehade
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Maheen Alam
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sarah Hassan
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Debabrata Maity
- Department of Chemistry, New York University, New York, NY, USA
| | - Liaqat Ali
- Core Technology Platforms, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mona Kalmouni
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Yamanappa Hunashal
- Chemistry Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.,DAME, Università di Udine, Udine, Italy
| | - Jemil Ahmed
- Department of Chemistry and Biochemistry and Knoebel Institute for Healthy Aging, The University of Denver, Denver, CO, USA
| | - Tatiana Houhou
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Shake Karapetyan
- Physics Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Zackary Falls
- Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), Buffalo, NY, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), Buffalo, NY, USA
| | - Renu Pasricha
- Core Technology Platforms, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Gennaro Esposito
- Chemistry Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.,INBB, Rome, Italy
| | - Ahmed J Afzal
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | | | - Sunil Kumar
- Department of Chemistry and Biochemistry and Knoebel Institute for Healthy Aging, The University of Denver, Denver, CO, USA.
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.
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16
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Johnson A, Stadlmeier M, Wühr M. TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level. J Proteome Res 2021; 20:3043-3052. [PMID: 33929851 DOI: 10.1021/acs.jproteome.0c00813] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiplexed proteomics is a powerful tool to assay cell states in health and disease, but accurate quantification of relative protein changes is impaired by interference from co-isolated peptides. Interference can be reduced by using MS3-based quantification, but this reduces sensitivity and requires specialized instrumentation. An alternative approach is quantification by complementary ions, the balancer group-peptide conjugates, which allows accurate and precise multiplexed quantification at the MS2 level and is compatible with most proteomics instruments. However, complementary ions of the popular TMT-tag form inefficiently and multiplexing is limited to five channels. Here, we evaluate and optimize complementary ion quantification for the recently released TMTpro-tag, which increases complementary ion plexing capacity to eight channels (TMTproC). Furthermore, the beneficial fragmentation properties of TMTpro increase sensitivity for TMTproC, resulting in ∼65% more proteins quantified compared to TMTpro-MS3 and ∼18% more when compared to real-time-search TMTpro-MS3 (RTS-SPS-MS3). TMTproC quantification is more accurate than TMTpro-MS2 and even superior to RTS-SPS-MS3. We provide the software for quantifying TMTproC data as an executable that is compatible with the MaxQuant analysis pipeline. Thus, TMTproC advances multiplexed proteomics data quality and widens access to accurate multiplexed proteomics beyond laboratories with MS3-capable instrumentation.
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Affiliation(s)
- Alex Johnson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States.,Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Michael Stadlmeier
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States.,Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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17
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Tran KV, Brown EL, DeSouza T, Jespersen NZ, Nandrup-Bus C, Yang Q, Yang Z, Desai A, Min SY, Rojas-Rodriguez R, Lundh M, Feizi A, Willenbrock H, Larsen TJ, Severinsen MCK, Malka K, Mozzicato AM, Deshmukh AS, Emanuelli B, Pedersen BK, Fitzgibbons T, Scheele C, Corvera S, Nielsen S. Human thermogenic adipocyte regulation by the long noncoding RNA LINC00473. Nat Metab 2020; 2:397-412. [PMID: 32440655 PMCID: PMC7241442 DOI: 10.1038/s42255-020-0205-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/14/2020] [Indexed: 02/07/2023]
Abstract
Human thermogenic adipose tissue mitigates metabolic disease, raising much interest in understanding its development and function. Here, we show that human thermogenic adipocytes specifically express a primate-specific long non-coding RNA, LINC00473 which is highly correlated with UCP1 expression and decreased in obesity and type-2 diabetes. LINC00473 is detected in progenitor cells, and increases upon differentiation and in response to cAMP. In contrast to other known adipocyte LincRNAs, LINC00473 shuttles out of the nucleus, colocalizes and can be crosslinked to mitochondrial and lipid droplet proteins. Up- or down- regulation of LINC00473 results in reciprocal alterations in lipolysis, respiration and transcription of genes associated with mitochondrial oxidative metabolism. Depletion of PLIN1 results in impaired cAMP-responsive LINC00473 expression and lipolysis, indicating bidirectional interactions between PLIN1, LINC00473 and mitochondrial oxidative functions. Thus, we suggest that LINC00473 is a key regulator of human thermogenic adipocyte function, and reveals a role for a LincRNA in inter-organelle communication and human energy metabolism.
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Affiliation(s)
- Khanh-Van Tran
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Erin L Brown
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Tiffany DeSouza
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Naja Zenius Jespersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie Nandrup-Bus
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Qin Yang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zinger Yang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anand Desai
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - So Yun Min
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Raziel Rojas-Rodriguez
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Morten Lundh
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Amir Feizi
- Novo Nordisk Research Centre Oxford, University of Oxford, Oxford, UK
| | - Hanni Willenbrock
- Novo Nordisk A/S, Discovery Biology & Technology Boinformatics, Maaloev, Denmark
| | - Therese Juhlin Larsen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Mai Charlotte Krogh Severinsen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kimberly Malka
- Department of Surgery, Division of Vascular and Endovascular Surgery, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anthony M Mozzicato
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Brice Emanuelli
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Timothy Fitzgibbons
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Camilla Scheele
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Silvia Corvera
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Søren Nielsen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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18
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Yu Q, Paulo JA, Naverrete-Perea J, McAlister GC, Canterbury JD, Bailey DJ, Robitaille AM, Huguet R, Zabrouskov V, Gygi SP, Schweppe DK. Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics. Anal Chem 2020; 92:6478-6485. [PMID: 32250601 DOI: 10.1021/acs.analchem.9b05685] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rise of sample multiplexing in quantitative proteomics for the dissection of complex phenotypic comparisons has been advanced by the development of ever more sensitive and robust instrumentation. Here, we evaluated the utility of the Orbitrap Eclipse Tribrid mass spectrometer (advanced quadrupole filter, optimized FTMS scan overhead) and new instrument control software features (Precursor Fit filtering, TurboTMT and Real-time Peptide Search filtering). Multidimensional comparisons of these novel features increased total peptide identifications by 20% for SPS-MS3 methods and 14% for HRMS2 methods. Importantly Real-time Peptide Search filtering enabled a ∼2× throughput improvement for quantification. Across the board, these sensitivity increases were attained without sacrificing quantitative accuracy. New hardware and software features enable more efficient characterization in pursuit of comparative whole proteome insights.
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Affiliation(s)
- Qing Yu
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | | | | | | | - Derek J Bailey
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Steven P Gygi
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Devin K Schweppe
- Harvard Medical School, Boston, Massachusetts 02115, United States
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19
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Bekker-Jensen DB, Martínez-Val A, Steigerwald S, Rüther P, Fort KL, Arrey TN, Harder A, Makarov A, Olsen JV. A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. Mol Cell Proteomics 2020; 19:716-729. [PMID: 32051234 PMCID: PMC7124470 DOI: 10.1074/mcp.tir119.001906] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Indexed: 12/31/2022] Open
Abstract
State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 min LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument, we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.
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Affiliation(s)
- Dorte B Bekker-Jensen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Ana Martínez-Val
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Sophia Steigerwald
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Patrick Rüther
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | | | | | | | | | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK.
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20
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Identifying drug targets in tissues and whole blood with thermal-shift profiling. Nat Biotechnol 2020; 38:303-308. [PMID: 31959954 DOI: 10.1038/s41587-019-0388-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022]
Abstract
Monitoring drug-target interactions with methods such as the cellular thermal-shift assay (CETSA) is well established for simple cell systems but remains challenging in vivo. Here we introduce tissue thermal proteome profiling (tissue-TPP), which measures binding of small-molecule drugs to proteins in tissue samples from drug-treated animals by detecting changes in protein thermal stability using quantitative mass spectrometry. We report organ-specific, proteome-wide thermal stability maps and derive target profiles of the non-covalent histone deacetylase inhibitor panobinostat in rat liver, lung, kidney and spleen and of the B-Raf inhibitor vemurafenib in mouse testis. In addition, we devised blood-CETSA and blood-TPP and applied it to measure target and off-target engagement of panobinostat and the BET family inhibitor JQ1 directly in whole blood. Blood-TPP analysis of panobinostat confirmed its binding to known targets and also revealed thermal stabilization of the zinc-finger transcription factor ZNF512. These methods will help to elucidate the mechanisms of drug action in vivo.
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21
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Mass Spectrometry-Based Biomarkers in Drug Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:435-449. [PMID: 31347063 DOI: 10.1007/978-3-030-15950-4_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Advances in mass spectrometry, proteomics, protein bioanalytical approaches, and biochemistry have led to a rapid evolution and expansion in the area of mass spectrometry-based biomarker discovery and development. The last decade has also seen significant progress in establishing accepted definitions, guidelines, and criteria for the analytical validation, acceptance and qualification of biomarkers. These advances have coincided with a decreased return on investment for pharmaceutical research and development and an increasing need for better early decision making tools. Empowering development teams with tools to measure a therapeutic interventions impact on disease state and progression, measure target engagement and to confirm predicted pharmacodynamic effects is critical to efficient data-driven decision making. Appropriate implementation of a biomarker or a combination of biomarkers can enhance understanding of a drugs mechanism, facilitate effective translation from the preclinical to clinical space, enable early proof of concept and dose selection, and increases the efficiency of drug development. Here we will provide descriptions of the different classes of biomarkers that have utility in the drug development process as well as review specific, protein-centric, mass spectrometry-based approaches for the discovery of biomarkers and development of targeted assays to measure these markers in a selective and analytically precise manner.
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