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Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583367. [PMID: 38496682 PMCID: PMC10942300 DOI: 10.1101/2024.03.04.583367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ~3500 proteins at a spatial resolution of 50 µm and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.
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Affiliation(s)
- Yumi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sarah M. Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ying Zhu
- Department of Proteomic and Genomic Technologies, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
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2
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Nitz AA, Giraldez Chavez JH, Eliason ZG, Payne SH. Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses. J Proteome Res 2024. [PMID: 38981598 DOI: 10.1021/acs.jproteome.4c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Single-cell analysis is an active area of research in many fields of biology. Measurements at single-cell resolution allow researchers to study diverse populations without losing biologically meaningful information to sample averages. Many technologies have been used to study single cells, including mass spectrometry-based single-cell proteomics (SCP). SCP has seen a lot of growth over the past couple of years through improvements in data acquisition and analysis, leading to greater proteomic depth. Because method development has been the main focus in SCP, biological applications have been sprinkled in only as proof-of-concept. However, SCP methods now provide significant coverage of the proteome and have been implemented in many laboratories. Thus, a primary question to address in our community is whether the current state of technology is ready for widespread adoption for biological inquiry. In this Perspective, we examine the potential for SCP in three thematic areas of biological investigation: cell annotation, developmental trajectories, and spatial mapping. We identify that the primary limitation of SCP is sample throughput. As proteome depth has been the primary target for method development to date, we advocate for a change in focus to facilitate measuring tens of thousands of single-cell proteomes to enable biological applications beyond proof-of-concept.
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Affiliation(s)
- Alyssa A Nitz
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
| | | | - Zachary G Eliason
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
| | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
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3
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Rhaman MS, Ali M, Ye W, Li B. Opportunities and Challenges in Advancing Plant Research with Single-cell Omics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae026. [PMID: 38996445 DOI: 10.1093/gpbjnl/qzae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 07/14/2024]
Abstract
Plants possess diverse cell types and intricate regulatory mechanisms to adapt to the ever-changing environment of nature. Various strategies have been employed to study cell types and their developmental progressions, including single-cell sequencing methods which provide high-dimensional catalogs to address biological concerns. In recent years, single-cell sequencing technologies in transcriptomics, epigenomics, proteomics, metabolomics, and spatial transcriptomics have been increasingly used in plant science to reveal intricate biological relationships at the single-cell level. However, the application of single-cell technologies to plants is more limited due to the challenges posed by cell structure. This review outlines the advancements in single-cell omics technologies, their implications in plant systems, future research applications, and the challenges of single-cell omics in plant systems.
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Affiliation(s)
- Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Wenxiu Ye
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
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4
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Xie X, Truong T, Huang S, Johnston SM, Hovanski S, Robinson A, Webber KGI, Lin HJL, Mun DG, Pandey A, Kelly RT. Multicolumn Nanoflow Liquid Chromatography with Accelerated Offline Gradient Generation for Robust and Sensitive Single-Cell Proteome Profiling. Anal Chem 2024; 96:10534-10542. [PMID: 38915247 DOI: 10.1021/acs.analchem.4c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Peptide separations that combine high sensitivity, robustness, peak capacity, and throughput are essential for extending bottom-up proteomics to smaller samples including single cells. To this end, we have developed a multicolumn nanoLC system with offline gradient generation. One binary pump generates gradients in an accelerated fashion to support multiple analytical columns, and a single trap column interfaces with all analytical columns to reduce required maintenance and simplify troubleshooting. A high degree of parallelization is possible, as one sample undergoes separation while the next sample plus its corresponding mobile phase gradient are transferred into the storage loop and a third sample is loaded into a sample loop. Selective offline elution from the trap column into the sample loop prevents salts and hydrophobic species from entering the analytical column, thus greatly enhancing column lifetime and system robustness. With this design, samples can be analyzed as fast as every 20 min at a flow rate of just 40 nL/min with close to 100% MS utilization time and continuously for as long as several months without column replacement. We utilized the system to analyze the proteomes of single cells from a multiple myeloma cell line upon treatment with the immunomodulatory imide drug lenalidomide.
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Affiliation(s)
- Xiaofeng Xie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
- MicrOmics Technologies, LLC, Spanish Fork, Utah 84660, United States
| | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
- MicrOmics Technologies, LLC, Spanish Fork, Utah 84660, United States
| | - Siqi Huang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Simon Hovanski
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Abigail Robinson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Hsien-Jung L Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
- MicrOmics Technologies, LLC, Spanish Fork, Utah 84660, United States
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5
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Montes C, Zhang J, Nolan TM, Walley JW. Single-cell proteomics differentiates Arabidopsis root cell types. THE NEW PHYTOLOGIST 2024. [PMID: 38923440 DOI: 10.1111/nph.19923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
Single-cell proteomics (SCP) is an emerging approach to resolve cellular heterogeneity within complex tissues of multi-cellular organisms. Here, we demonstrate the feasibility of SCP on plant samples using the model plant Arabidopsis thaliana. Specifically, we focused on examining isolated single cells from the cortex and endodermis, which are two adjacent root cell types derived from a common stem cell lineage. From 756 root cells, we identified 3763 proteins and 1118 proteins/cell. Ultimately, we focus on 3217 proteins quantified following stringent filtering. Of these, we identified 596 proteins whose expression is enriched in either the cortex or endodermis and are able to differentiate these closely related plant cell types. Collectivity, this study demonstrates that SCP can resolve neighboring cell types with distinct functions, thereby facilitating the identification of biomarkers and candidate proteins to enable functional genomics.
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Affiliation(s)
- Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Jingyuan Zhang
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011, USA
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6
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Martin KR, Le HT, Abdelgawad A, Yang C, Lu G, Keffer JL, Zhang X, Zhuang Z, Asare-Okai PN, Chan CS, Batish M, Yu Y. Development of an efficient, effective, and economical technology for proteome analysis. CELL REPORTS METHODS 2024; 4:100796. [PMID: 38866007 PMCID: PMC11228373 DOI: 10.1016/j.crmeth.2024.100796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/21/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome.
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Affiliation(s)
- Katherine R Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ahmed Abdelgawad
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Canyuan Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Guotao Lu
- CDS Analytical, LLC, Oxford, PA 19363, USA
| | - Jessica L Keffer
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA
| | | | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Papa Nii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA; School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA.
| | - Yanbao Yu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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7
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Roberts DS, Loo JA, Tsybin YO, Liu X, Wu S, Chamot-Rooke J, Agar JN, Paša-Tolić L, Smith LM, Ge Y. Top-down proteomics. NATURE REVIEWS. METHODS PRIMERS 2024; 4:38. [PMID: 39006170 PMCID: PMC11242913 DOI: 10.1038/s43586-024-00318-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 07/16/2024]
Abstract
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is essential to unravel the intricacies of biological systems and bridge the gap between genotypes and phenotypes. By analysing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and can decipher protein function, uncover disease mechanisms and advance precision medicine. This Primer explores TDP, including the underlying principles, recent advances and an outlook on the future. The experimental section discusses instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques and data collection. The results section looks at how to decipher raw data, visualize intact protein spectra and unravel data analysis. Additionally, proteoform identification, characterization and quantification are summarized, alongside approaches for statistical analysis. Various applications are described, including the human proteoform project and biomedical, biopharmaceutical and clinical sciences. These are complemented by discussions on measurement reproducibility, limitations and a forward-looking perspective that outlines areas where the field can advance, including potential future applications.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California - Los Angeles, Los Angeles, CA, USA
| | | | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | | | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, Human Proteomics Program, University of Wisconsin - Madison, Madison, WI, USA
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8
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Adnane M, de Almeida AM, Chapwanya A. Unveiling the power of proteomics in advancing tropical animal health and production. Trop Anim Health Prod 2024; 56:182. [PMID: 38825622 DOI: 10.1007/s11250-024-04037-4] [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: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/04/2024]
Abstract
Proteomics, the large-scale study of proteins in biological systems has emerged as a pivotal tool in the field of animal and veterinary sciences, mainly for investigating local and rustic breeds. Proteomics provides valuable insights into biological processes underlying animal growth, reproduction, health, and disease. In this review, we highlight the key proteomics technologies, methodologies, and their applications in domestic animals, particularly in the tropical context. We also discuss advances in proteomics research, including integration of multi-omics data, single-cell proteomics, and proteogenomics, all of which are promising for improving animal health, adaptation, welfare, and productivity. However, proteomics research in domestic animals faces challenges, such as sample preparation variation, data quality control, privacy and ethical considerations relating to animal welfare. We also provide recommendations for overcoming these challenges, emphasizing the importance of following best practices in sample preparation, data quality control, and ethical compliance. We therefore aim for this review to harness the full potential of proteomics in advancing our understanding of animal biology and ultimately improve animal health and productivity in local breeds of diverse animal species in a tropical context.
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Affiliation(s)
- Mounir Adnane
- Department of Biomedicine, Institute of Veterinary Sciences, University of Tiaret, Tiaret, 14000, Algeria.
| | - André M de Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, 1349-017, Portugal
| | - Aspinas Chapwanya
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, 00265, Saint Kitts and Nevis
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9
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Yang Z, Jin K, Chen Y, Liu Q, Chen H, Hu S, Wang Y, Pan Z, Feng F, Shi M, Xie H, Ma H, Zhou H. AM-DMF-SCP: Integrated Single-Cell Proteomics Analysis on an Active Matrix Digital Microfluidic Chip. JACS AU 2024; 4:1811-1823. [PMID: 38818059 PMCID: PMC11134390 DOI: 10.1021/jacsau.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 06/01/2024]
Abstract
Single-cell proteomics offers unparalleled insights into cellular diversity and molecular mechanisms, enabling a deeper understanding of complex biological processes at the individual cell level. Here, we develop an integrated sample processing on an active-matrix digital microfluidic chip for single-cell proteomics (AM-DMF-SCP). Employing the AM-DMF-SCP approach and data-independent acquisition (DIA), we identify an average of 2258 protein groups in single HeLa cells within 15 min of the liquid chromatography gradient. We performed comparative analyses of three tumor cell lines: HeLa, A549, and HepG2, and machine learning was utilized to identify the unique features of these cell lines. Applying the AM-DMF-SCP to characterize the proteomes of a third-generation EGFR inhibitor, ASK120067-resistant cells (67R) and their parental NCI-H1975 cells, we observed a potential correlation between elevated VIM expression and 67R resistance, which is consistent with the findings from bulk sample analyses. These results suggest that AM-DMF-SCP is an automated, robust, and sensitive platform for single-cell proteomics and demonstrate the potential for providing valuable insights into cellular mechanisms.
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Affiliation(s)
- Zhicheng Yang
- Department
of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
- University
of the Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Jin
- CAS
Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy
of Sciences, Suzhou 215163, China
| | - Yimin Chen
- Department
of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
- University
of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Liu
- Department
of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| | - Hongxu Chen
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Siyi Hu
- CAS
Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy
of Sciences, Suzhou 215163, China
| | - Yuqiu Wang
- Department
of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| | - Zilu Pan
- Division
of Antitumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fang Feng
- Division
of Antitumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mude Shi
- Guangdong
ACXEL Micro & Nano Tech Co. Ltd., Foshan, Guangdong Province 528000, China
| | - Hua Xie
- University
of the Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan
Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- Division
of Antitumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hanbin Ma
- CAS
Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy
of Sciences, Suzhou 215163, China
- Guangdong
ACXEL Micro & Nano Tech Co. Ltd., Foshan, Guangdong Province 528000, China
| | - Hu Zhou
- Department
of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
- University
of the Chinese Academy of Sciences, Beijing 100049, China
- Hangzhou
Institute for Advanced Study, University
of Chinese Academy of Sciences, Hangzhou 310024, China
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10
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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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11
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Marie AL, Gao Y, Ivanov AR. Native N-glycome profiling of single cells and ng-level blood isolates using label-free capillary electrophoresis-mass spectrometry. Nat Commun 2024; 15:3847. [PMID: 38719792 PMCID: PMC11079027 DOI: 10.1038/s41467-024-47772-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we present an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased quantitative characterization of single-cell surface N-glycomes are demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations are unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow is also applied to the profiling of ng-level amounts (5-500 ng) of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.
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Affiliation(s)
- Anne-Lise Marie
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Yunfan Gao
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US.
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12
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Khan S, Conover R, Asthagiri AR, Slavov N. Dynamics of Single-Cell Protein Covariation during Epithelial-Mesenchymal Transition. J Proteome Res 2024. [PMID: 38663020 DOI: 10.1021/acs.jproteome.4c00277] [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] [Indexed: 05/02/2024]
Abstract
Physiological processes, such as the epithelial-mesenchymal transition (EMT), are mediated by changes in protein interactions. These changes may be better reflected in protein covariation within a cellular cluster than in the temporal dynamics of cluster-average protein abundance. To explore this possibility, we quantified proteins in single human cells undergoing EMT. Covariation analysis of the data revealed that functionally coherent protein clusters dynamically changed their protein-protein correlations without concomitant changes in the cluster-average protein abundance. These dynamics of protein-protein correlations were monotonic in time and delineated protein modules functioning in actin cytoskeleton organization, energy metabolism, and protein transport. These protein modules are defined by protein covariation within the same time point and cluster and, thus, reflect biological regulation masked by the cluster-average protein dynamics. Thus, protein correlation dynamics across single cells offers a window into protein regulation during physiological transitions.
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Affiliation(s)
- Saad Khan
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rachel Conover
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Anand R Asthagiri
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Parallel Squared Technology Institute, Watertown, Massachusetts 02472, United States
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13
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Khan S, Conover R, Asthagiri AR, Slavov N. Dynamics of single-cell protein covariation during epithelial-mesenchymal transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572913. [PMID: 38187715 PMCID: PMC10769332 DOI: 10.1101/2023.12.21.572913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Physiological processes, such as epithelial-mesenchymal transition (EMT), are mediated by changes in protein interactions. These changes may be better reflected in protein covariation within cellular cluster than in the temporal dynamics of cluster-average protein abundance. To explore this possibility, we quantified proteins in single human cells undergoing EMT. Covariation analysis of the data revealed that functionally coherent protein clusters dynamically changed their protein-protein correlations without concomitant changes in cluster-average protein abundance. These dynamics of protein-protein correlations were monotonic in time and delineated protein modules functioning in actin cytoskeleton organization, energy metabolism and protein transport. These protein modules are defined by protein covariation within the same time point and cluster and thus reflect biological regulation masked by the cluster-average protein dynamics. Thus, protein correlation dynamics across single cells offer a window into protein regulation during physiological transitions.
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Affiliation(s)
- Saad Khan
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Rachel Conover
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Anand R. Asthagiri
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Biology, Northeastern University, Boston, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Biology, Northeastern University, Boston, MA, USA
- Parallel Squared Technology Institute, Watertown, MA 02472, USA
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14
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Truong T, Kelly RT. What's new in single-cell proteomics. Curr Opin Biotechnol 2024; 86:103077. [PMID: 38359605 PMCID: PMC11068367 DOI: 10.1016/j.copbio.2024.103077] [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: 10/27/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
In recent years, single-cell proteomics (SCP) has advanced significantly, enabling the analysis of thousands of proteins within single mammalian cells. This progress is driven by advances in experimental design, with maturing label-free and multiplexed methods, optimized sample preparation, and innovations in separation techniques, including ultra-low-flow nanoLC. These factors collectively contribute to improved sensitivity, throughput, and reproducibility. Cutting-edge mass spectrometry platforms and data acquisition approaches continue to play a critical role in enhancing data quality. Furthermore, the exploration of spatial proteomics with single-cell resolution offers significant promise for understanding cellular interactions, giving rise to various phenotypes. SCP has far-reaching applications in cancer research, biomarker discovery, and developmental biology. Here, we provide a critical review of recent advances in the field of SCP.
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Affiliation(s)
- Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States.
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15
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Webber KGI, Huang S, Truong T, Heninger JL, Gregus M, Ivanov AR, Kelly RT. Open-tubular trap columns: towards simple and robust liquid chromatography separations for single-cell proteomics. Mol Omics 2024; 20:184-191. [PMID: 38353725 PMCID: PMC10963139 DOI: 10.1039/d3mo00249g] [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: 03/07/2024]
Abstract
Nanoflow liquid chromatography-mass spectrometry is key to enabling in-depth proteome profiling of trace samples, including single cells, but these separations can lack robustness due to the use of narrow-bore columns that are susceptible to clogging. In the case of single-cell proteomics, offline cleanup steps are generally omitted to avoid losses to additional surfaces, and online solid-phase extraction/trap columns frequently provide the only opportunity to remove salts and insoluble debris before the sample is introduced to the analytical column. Trap columns are traditionally short, packed columns used to load and concentrate analytes at flow rates greater than those employed in analytical columns, and since these first encounter the uncleaned sample mixture, trap columns are also susceptible to clogging. We hypothesized that clogging could be avoided by using large-bore porous layer open tubular trap columns (PLOTrap). The low back pressure ensured that the PLOTraps could also serve as the sample loop, thus allowing sample cleanup and injection with a single 6-port valve. We found that PLOTraps could effectively remove debris to avoid column clogging. We also evaluated multiple stationary phases and PLOTrap diameters to optimize performance in terms of peak widths and sample loading capacities. Optimized PLOTraps were compared to conventional packed trap columns operated in forward and backflush modes, and were found to have similar chromatographic performance of backflushed traps while providing improved debris removal for robust analysis of trace samples.
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Affiliation(s)
- Kei G I Webber
- Brigham Young University, Department of Chemistry and Biochemistry, Provo, Utah, 84602, USA.
| | - Siqi Huang
- Brigham Young University, Department of Chemistry and Biochemistry, Provo, Utah, 84602, USA.
| | - Thy Truong
- Brigham Young University, Department of Chemistry and Biochemistry, Provo, Utah, 84602, USA.
| | - Jacob L Heninger
- Brigham Young University, Department of Chemistry and Biochemistry, Provo, Utah, 84602, USA.
| | - Michal Gregus
- Northeastern University, Barnett Institute of Biological and Chemical Analysis, Department of Chemistry and Chemical Biology, College of Science, Boston, MA 02115, USA
| | - Alexander R Ivanov
- Northeastern University, Barnett Institute of Biological and Chemical Analysis, Department of Chemistry and Chemical Biology, College of Science, Boston, MA 02115, USA
| | - Ryan T Kelly
- Brigham Young University, Department of Chemistry and Biochemistry, Provo, Utah, 84602, USA.
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16
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Zhu T, Li S, Liu D, Zhang X, Zhou L, Zhou R, Yang B. Single-worm quantitative proteomics reveals aging heterogeneity in isogenic Caenorhabditis elegans. Aging Cell 2024; 23:e14055. [PMID: 38044578 PMCID: PMC10928571 DOI: 10.1111/acel.14055] [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: 06/26/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
The heterogeneity of aging has been investigated at cellular and organic levels in the mouse model and human, but the exploration of aging heterogeneity at whole-organism level is lacking. C. elegans is an ideal model organism for studying this question as they are self-fertilized and cultured in the same chamber. Despite the tremendous progress made in single-cell proteomic analysis, there is few single-worm proteomics studies about aging. Here, we apply single-worm quantitative mass spectrometry to quantify the heterogenous proteomic changes during aging across individuals, a total of 3524 proteins from 157 C. eleagns individuals were quantified. A reconstructed C. elegans aging trajectory and proteomic landscape of fast-aging individuals were used to analyze the heterogeneity of C. elegans aging. We characterized inter-individual proteomic variation during aging and revealed contributing factors that distinguish fast-aging individuals from their siblings.
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Affiliation(s)
- Tian‐Yi Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | | | - Dan‐Dan Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Xiajun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Rong Zhou
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
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17
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Shen B, Pade LR, Nemes P. The 15-min (Sub)Cellular Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580399. [PMID: 38405838 PMCID: PMC10888744 DOI: 10.1101/2024.02.15.580399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Single-cell mass spectrometry (MS) opens a proteomic window onto the inner workings of cells. Here, we report the discovery characterization of the subcellular proteome of single, identified embryonic cells in record speed and molecular coverage. We integrated subcellular capillary microsampling, fast capillary electrophoresis (CE), high-efficiency nano-flow electrospray ionization, and orbitrap tandem MS. In proof-of-principle tests, we found shorter separation times to hinder proteome detection using DDA, but not DIA. Within a 15-min effective separation window, CE data-independent acquisition (DIA) was able to identify 1,161 proteins from single HeLa-cell-equivalent (∼200 pg) proteome digests vs. 401 proteins by the reference data-dependent acquisition (DDA) on the same platform. The approach measured 1,242 proteins from subcellular niches in an identified cell in the live Xenopus laevis (frog) embryo, including many canonical components of organelles. CE-MS with DIA enables fast, sensitive, and deep profiling of the (sub)cellular proteome, expanding the bioanalytical toolbox of cell biology. Authorship Contributions P.N. and B.S. designed the study. L.R.P. collected the X. laevis cell aspirates. B.S. prepared and measured the samples. B.S. and P.N. analyzed the data and interpreted the results. P.N. and B.S. wrote the manuscript. All the authors commented on the manuscript.
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18
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Wang Y, Guan ZY, Shi SW, Jiang YR, Zhang J, Yang Y, Wu Q, Wu J, Chen JB, Ying WX, Xu QQ, Fan QX, Wang HF, Zhou L, Wang L, Fang J, Pan JZ, Fang Q. Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell. Nat Commun 2024; 15:1279. [PMID: 38341466 PMCID: PMC10858870 DOI: 10.1038/s41467-024-45659-4] [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: 10/09/2022] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of ~1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a mammalian cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 2449-3500, 2278-3257 and 1621-2904 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27) under the DIA (MBR) mode, respectively. Benefiting from the flexible cell picking-up ability, we study HeLa cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.
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Affiliation(s)
- Yu Wang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, China
| | - Zhi-Ying Guan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Shao-Wen Shi
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Yi-Rong Jiang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jie Zhang
- Department of Cell Biology, China Medical University, Shenyang, 110122, China
| | - Yi Yang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Qiong Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jie Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Bo Chen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Wei-Xin Ying
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qin-Qin Xu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Xi Fan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Feng Wang
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Li Zhou
- Shanghai Omicsolution Co., Shanghai, 201100, China
| | - Ling Wang
- Shanghai Omicsolution Co., Shanghai, 201100, China
| | - Jin Fang
- Department of Cell Biology, China Medical University, Shenyang, 110122, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China.
- Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou, 310007, China.
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19
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Matzinger M, Schmücker A, Yelagandula R, Stejskal K, Krššáková G, Berger F, Mechtler K, Mayer RL. Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications. Nat Commun 2024; 15:1019. [PMID: 38310095 PMCID: PMC10838342 DOI: 10.1038/s41467-024-45391-z] [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: 03/02/2023] [Accepted: 01/19/2024] [Indexed: 02/05/2024] Open
Abstract
Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.
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Affiliation(s)
- Manuel Matzinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Anna Schmücker
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ramesh Yelagandula
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Gabriela Krššáková
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| | - Rupert L Mayer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
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20
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Ziegler AR, Dufour A, Scott NE, Edgington-Mitchell LE. Ion Mobility-Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen. Mol Cell Proteomics 2024; 23:100714. [PMID: 38199506 PMCID: PMC10862022 DOI: 10.1016/j.mcpro.2024.100714] [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: 07/28/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Aberrant levels of the asparaginyl endopeptidase legumain have been linked to inflammation, neurodegeneration, and cancer, yet our understanding of this protease is incomplete. Systematic attempts to identify legumain substrates have been previously confined to in vitro studies, which fail to mirror physiological conditions and obscure biologically relevant cleavage events. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS), we developed a streamlined approach for proteome and N-terminome analyses without the need for N-termini enrichment. Compared to unfractionated proteomic analysis, we demonstrate FAIMS fractionation improves N-termini identification by >2.5 fold, resulting in the identification of >2882 unique N-termini from limited sample amounts. In murine spleens, this approach identifies 6366 proteins and 2528 unique N-termini, with 235 cleavage events enriched in WT compared to legumain-deficient spleens. Among these, 119 neo-N-termini arose from asparaginyl endopeptidase activities, representing novel putative physiological legumain substrates. The direct cleavage of selected substrates by legumain was confirmed using in vitro assays, providing support for the existence of physiologically relevant extra-lysosomal legumain activity. Combined, these data shed critical light on the functions of legumain and demonstrate the utility of FAIMS as an accessible method to improve depth and quality of N-terminomics studies.
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Affiliation(s)
- Alexander R Ziegler
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute, The University of Melbourne, Parkville, Victoria, Australia.
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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21
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Tian X, Hopfgartner G. Improved quantification of carbonyl sub-metabolome by liquid chromatography mass spectrometry using a fragment controlled multiplexed isotopic tag. Anal Chim Acta 2024; 1287:342117. [PMID: 38182390 DOI: 10.1016/j.aca.2023.342117] [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: 08/07/2023] [Revised: 11/03/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Carbonyl-containing metabolites are a class of key intermediate in metabolism, which has potentials to be biomarkers. Since their poor ionization, derivatization reagents, such as dansylhydrazine, are usually used to improve the sensitivity and/or to facilitate quantification. However, most current carbonyl derivatization reagents only have two channels, one is isotopically labeled and the other one is non-labeled. To quantify more samples in a run and using data-independent acquisition (DIA) mode to get comprehensive and unbiased mass fragmentation, we proposed a fragment-controlled isotopic tag, called DiMe-FP-NHNH2 (FP) which has five channels: Δ0, Δ3, Δ6, Δ9, and Δ12, thus up to 5 samples can be analyzed in a run. RESULTS The most important improvement is that the FP tag can produce multiple characteristic signals in tandem mass, diagnostic ions and neutral losses, which helps to selectively detect aldehydes/ketones for targeted and untargeted analysis. To exhibit all capabilities of the FP tag, we mimicked an untargeted metabolomics experiment, which comprises two steps. First, discovery step, using Data-Independent Analysis (SWATH-MS) and the labeling of two channels (Δ0 and Δ3), we picked out aldehyde/ketone from the pooled urine samples based on three characteristic signals, including isotope patterns, diagnostic ions, and neutral losses. Second, five-plex quantification, relative and absolute quantification were achieved in a single LC-MS analysis. Notably, because of different nominal masses, the FP tag can be used on any low or high resolution mass spectrometers. SIGNIFICANCE The benefits and performance of the FP tag are demonstrated by the analysis of urine samples collected from patients from a prostate cancer study, in which more than a thousand features were found based on MS1 fingerprint, but only around 120 aldehyde/ketone candidates were confirmed with characteristic signals and nine of which were quantified showing significant differences from healthy and reference urine samples.
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Affiliation(s)
- Xiaobo Tian
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva 4, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva 4, Switzerland.
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22
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Guise AJ, Misal SA, Carson R, Chu JH, Boekweg H, Van Der Watt D, Welsh NC, Truong T, Liang Y, Xu S, Benedetto G, Gagnon J, Payne SH, Plowey ED, Kelly RT. TDP-43-stratified single-cell proteomics of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis. Cell Rep 2024; 43:113636. [PMID: 38183652 PMCID: PMC10926001 DOI: 10.1016/j.celrep.2023.113636] [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: 06/07/2023] [Revised: 11/02/2023] [Accepted: 12/14/2023] [Indexed: 01/08/2024] Open
Abstract
A limitation of conventional bulk-tissue proteome studies in amyotrophic lateral sclerosis (ALS) is the confounding of motor neuron (MN) signals by admixed non-MN proteins. Here, we leverage laser capture microdissection and nanoPOTS single-cell mass spectrometry-based proteomics to query changes in protein expression in single MNs from postmortem ALS and control tissues. In a follow-up analysis, we examine the impact of stratification of MNs based on cytoplasmic transactive response DNA-binding protein 43 (TDP-43)+ inclusion pathology on the profiles of 2,238 proteins. We report extensive overlap in differentially abundant proteins identified in ALS MNs with or without overt TDP-43 pathology, suggesting early and sustained dysregulation of cellular respiration, mRNA splicing, translation, and vesicular transport in ALS. Together, these data provide insights into proteome-level changes associated with TDP-43 proteinopathy and begin to demonstrate the utility of pathology-stratified trace sample proteomics for understanding single-cell protein dynamics in human neurologic diseases.
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Affiliation(s)
| | - Santosh A Misal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | - Hannah Boekweg
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | | | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | | | | | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
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23
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [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] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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24
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Truong T, Sanchez-Avila X, Webber KGI, Johnston SM, Kelly RT. Efficient and Sensitive Sample Preparation, Separations, and Data Acquisition for Label-Free Single-Cell Proteomics. Methods Mol Biol 2024; 2817:67-84. [PMID: 38907148 DOI: 10.1007/978-1-0716-3934-4_7] [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: 06/23/2024]
Abstract
We describe a sensitive and efficient workflow for label-free single-cell proteomics that spans sample preparation, liquid chromatography separations, and mass spectrometry data acquisition. The Tecan Uno Single Cell Dispenser provides rapid cell isolation and nanoliter-volume reagent dispensing within 384-well PCR plates. A newly developed sample processing workflow achieves cell lysis, protein denaturation, and digestion in 1 h with a single reagent dispensing step. Low-flow liquid chromatography coupled with wide-window data-dependent acquisition results in the quantification of nearly 3000 proteins per cell using an Orbitrap Exploris 480 mass spectrometer. This approach greatly broadens accessibility to sensitive single-cell proteome profiling for nonspecialist laboratories.
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Affiliation(s)
- Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Ximena Sanchez-Avila
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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25
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Zhang D, Qiao L. Microfluidics Coupled Mass Spectrometry for Single Cell Multi-Omics. SMALL METHODS 2024; 8:e2301179. [PMID: 37840412 DOI: 10.1002/smtd.202301179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Population-level analysis masks significant heterogeneity between individual cells, making it difficult to accurately reflect the true intricacies of life activities. Microfluidics is a technique that can manipulate individual cells effectively and is commonly coupled with a variety of analytical methods for single-cell analysis. Single-cell omics provides abundant molecular information at the single-cell level, fundamentally revealing differences in cell types and biological states among cell individuals, leading to a deeper understanding of cellular phenotypes and life activities. Herein, this work summarizes the microfluidic chips designed for single-cell isolation, manipulation, trapping, screening, and sorting, including droplet microfluidic chips, microwell arrays, hydrodynamic microfluidic chips, and microchips with microvalves. This work further reviews the studies on single-cell proteomics, metabolomics, lipidomics, and multi-omics based on microfluidics and mass spectrometry. Finally, the challenges and future application of single-cell multi-omics are discussed.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
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26
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Mayer RL, Mechtler K. Immunopeptidomics in the Era of Single-Cell Proteomics. BIOLOGY 2023; 12:1514. [PMID: 38132340 PMCID: PMC10740491 DOI: 10.3390/biology12121514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. The field has made tremendous strides over the last 25 years but currently still faces challenges in sensitivity and throughput for widespread applications in personalized medicine and large vaccine development studies. Cutting-edge technological advancements in sample preparation, liquid chromatography as well as mass spectrometry, and data analysis, however, are currently transforming the field. This perspective showcases how the advent of single-cell proteomics has accelerated this transformation of immunopeptidomics in recent years and will pave the way for even more sensitive and higher-throughput immunopeptidomics analyses.
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Affiliation(s)
- Rupert L. Mayer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, 1030 Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
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27
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Wu C, Lei J, Meng F, Wang X, Wong CJ, Peng J, Lin G, Gingras AC, Ma J, Zhang S. Trace Sample Proteome Quantification by Data-Dependent Acquisition without Dynamic Exclusion. Anal Chem 2023; 95:17981-17987. [PMID: 38032138 PMCID: PMC10719888 DOI: 10.1021/acs.analchem.3c03357] [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] [Received: 07/28/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023]
Abstract
Despite continuous technological improvements in sample preparation, mass-spectrometry-based proteomics for trace samples faces the challenges of sensitivity, quantification accuracy, and reproducibility. Herein, we explored the applicability of turboDDA (a method that uses data-dependent acquisition without dynamic exclusion) for quantitative proteomics of trace samples. After systematic optimization of acquisition parameters, we compared the performance of turboDDA with that of data-dependent acquisition with dynamic exclusion (DEDDA). By benchmarking the analysis of trace unlabeled human cell digests, turboDDA showed substantially better sensitivity in comparison with DEDDA, whether for unfractionated or high pH fractionated samples. Furthermore, through designing an iTRAQ-labeled three-proteome model (i.e., tryptic digest of protein lysates from yeast, human, and E. coli) to document the interference effect, we evaluated the quantification interference, accuracy, reproducibility of iTRAQ labeled trace samples, and the impact of PIF (precursor intensity fraction) cutoff for different approaches (turboDDA and DEDDA). The results showed that improved quantification accuracy and reproducibility could be achieved by turboDDA, while a more stringent PIF cutoff resulted in more accurate quantification but less peptide identification for both approaches. Finally, the turboDDA strategy was applied to the differential analysis of limited amounts of human lung cancer cell samples, showing great promise in trace proteomics sample analysis.
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Affiliation(s)
- Ci Wu
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20007, United States
| | - Jiao Lei
- Clinical
Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan 410000, China
| | - Fei Meng
- Clinical
Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan 410000, China
| | - Xingyao Wang
- National
& Local Joint Engineering Laboratory of Animal Peptide Drug Development,
College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Cassandra J. Wong
- Lunenfeld-Tanenbaum
Research Institute, Toronto, Ontario M5G 1X5, Canada
| | - Jiaxi Peng
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Ge Lin
- Clinical
Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan 410000, China
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum
Research Institute, Toronto, Ontario M5G 1X5, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Junfeng Ma
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20007, United States
| | - Shen Zhang
- Clinical
Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan 410000, China
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28
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Ctortecka C, Hartlmayr D, Seth A, Mendjan S, Tourniaire G, Udeshi ND, Carr SA, Mechtler K. An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity. Mol Cell Proteomics 2023; 22:100665. [PMID: 37839701 PMCID: PMC10684380 DOI: 10.1016/j.mcpro.2023.100665] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023] Open
Abstract
Multiplexed and label-free mass spectrometry-based approaches with single-cell resolution have attributed surprising heterogeneity to presumed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lags. Here, we introduce the proteoCHIP, a universal option for single-cell proteomics sample preparation including multiplexed labeling up to 16-plex with high sensitivity and throughput. The automated processing using a commercial system combining single-cell isolation and picoliter dispensing, the cellenONE, reduces final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error-prone manual sample handling and overcoming evaporation. The specialized proteoCHIP design allows direct injection of single cells via a standard autosampler resulting in around 1500 protein groups per TMT10-plex with reduced or eliminated need for a carrier proteome. We evaluated the effect of wider precursor isolation windows at single-cell input levels and found that using 2 Da isolation windows increased overall sensitivity without significantly impacting interference. Using the dedicated mass spectrometry acquisition strategies detailed here, we identified on average close to 2000 proteins per TMT10-plex across 170 multiplexed single cells that readily distinguished human cell types. Overall, our workflow combines highly efficient sample preparation, chromatographic and ion mobility-based filtering, rapid wide-window data-dependent acquisition analysis, and intelligent data analysis for optimal multiplexed single-cell proteomics. This versatile and automated proteoCHIP-based sample preparation approach is sufficiently sensitive to drive biological applications of single-cell proteomics and can be readily adopted by proteomics laboratories.
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Affiliation(s)
- Claudia Ctortecka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
| | - David Hartlmayr
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Cellenion SASU, Lyon, France
| | | | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | | | - Namrata D Udeshi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Cellenion SASU, Lyon, France; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria; The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria.
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29
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Cooke JP, Lai L. Transflammation in tissue regeneration and response to injury: How cell-autonomous inflammatory signaling mediates cell plasticity. Adv Drug Deliv Rev 2023; 203:115118. [PMID: 37884127 PMCID: PMC10842620 DOI: 10.1016/j.addr.2023.115118] [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: 10/18/2022] [Revised: 08/01/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
Inflammation is a first responder against injury and infection and is also critical for the regeneration and repair of tissue after injury. The role of professional immune cells in tissue healing is well characterized. Professional immune cells respond to pathogens with humoral and cytotoxic responses; remove cellular debris through efferocytosis; secrete angiogenic cytokines and growth factors to repair the microvasculature and parenchyma. However, non-immune cells are also capable of responding to damage or pathogens. Non-immune somatic cells express pattern recognition receptors (PRRs) to detect pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs). The PRRs activation leads to the release of inflammatory cytokines required for tissue defense and repair. Notably, the activation of PRRs also triggers epigenetic changes that promote DNA accessibility and cellular plasticity. Thus, non-immune cells directly respond to the local inflammatory cues and can undergo phenotypic modifications or even cell lineage transitions to facilitate tissue regeneration. This review will focus on the novel role of cell-autonomous inflammatory signaling in mediating cell plasticity, a process which is termed transflammation. We will discuss the regulation of this process by changes in the functions and expression levels of epigenetic modifiers, as well as metabolic and ROS/RNS-mediated epigenetic modulation of DNA accessibility during cell fate transition. We will highlight the recent technological developments in detecting cell plasticity and potential therapeutic applications of transflammation in tissue regeneration.
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Affiliation(s)
- John P Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Li Lai
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States.
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30
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He Y, Yuan H, Liang Y, Liu X, Zhang X, Ji Y, Zhao B, Yang K, Zhang J, Zhang S, Zhang Y, Zhang L. On-capillary alkylation micro-reactor: a facile strategy for proteo-metabolome profiling in the same single cells. Chem Sci 2023; 14:13495-13502. [PMID: 38033888 PMCID: PMC10686037 DOI: 10.1039/d3sc05047e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Single-cell multi-omics analysis can provide comprehensive insights to study cell-to-cell heterogeneity in normal and disease physiology. However, due to the lack of amplification technique, the measurement of proteome and metabolome in the same cell is challenging. Herein, a novel on-capillary alkylation micro-reactor (OCAM) was developed to achieve proteo-metabolome profiling in the same single cells, by which proteins were first covalently bound to an iodoacetic acid functionalized open-tubular capillary micro-reactor via sulfhydryl alkylation reaction, and metabolites were rapidly eluted, followed by on-column digestion of captured proteins. Compared with existing methods for low-input proteome sample preparation, OCAM exhibited improved efficiency, anti-interference ability and recovery, enabling the identification of an average of 1509 protein groups in single HeLa cells. This strategy was applied to single-cell proteo-metabolome analysis of mouse oocytes at different stages, 3457 protein groups and 171 metabolites were identified in single oocytes, which is the deepest coverage of proteome and metabolome from single mouse oocytes to date, achieving complementary characterization of metabolic patterns during oocyte maturation.
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Affiliation(s)
- Yingyun He
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yu Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Xinxin Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Xiaozhe Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yahui Ji
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Jue Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha 410013 China
| | - Shen Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha 410013 China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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31
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Jiang YR, Zhu L, Cao LR, Wu Q, Chen JB, Wang Y, Wu J, Zhang TY, Wang ZL, Guan ZY, Xu QQ, Fan QX, Shi SW, Wang HF, Pan JZ, Fu XD, Wang Y, Fang Q. Simultaneous deep transcriptome and proteome profiling in a single mouse oocyte. Cell Rep 2023; 42:113455. [PMID: 37976159 DOI: 10.1016/j.celrep.2023.113455] [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: 12/10/2022] [Revised: 09/23/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform based on microfluidics, high-throughput sequencing, and mass spectrometry technology to achieve deep and joint quantitative analysis of transcriptome and proteome at the single-cell level, providing an important resource for understanding the relationship between transcription and translation in cells. This platform was applied to analyze single mouse oocytes at different meiotic maturation stages, reaching an average quantification depth of 19,948 genes and 2,663 protein groups in single mouse oocytes. In particular, we analyzed the correlation of individual RNA and protein pairs, as well as the meiosis regulatory network with unprecedented depth, and identified 30 transcript-protein pairs as specific oocyte maturational signatures, which could be productive for exploring transcriptional and translational regulatory features during oocyte meiosis.
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Affiliation(s)
- Yi-Rong Jiang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Le Zhu
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China
| | - Lan-Rui Cao
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China
| | - Qiong Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jian-Bo Chen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Jie Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | | | | | - Zhi-Ying Guan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qin-Qin Xu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qian-Xi Fan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Shao-Wen Shi
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Hui-Feng Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Xu-Dong Fu
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China; Center of Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310011, China.
| | - Yongcheng Wang
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China; Department of Laboratory Medicine, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310011, China.
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China; Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou 310007, China.
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32
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Ivanov A, Marie AL, Gao Y. In-capillary sample processing coupled to label-free capillary electrophoresis-mass spectrometry to decipher the native N-glycome of single mammalian cells and ng-level blood isolates. RESEARCH SQUARE 2023:rs.3.rs-3500983. [PMID: 38014012 PMCID: PMC10680937 DOI: 10.21203/rs.3.rs-3500983/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we developed an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased characterization and quantification of single-cell surface N-glycomes were demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations were unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow was also applied to the profiling of ng-level amounts of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.
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33
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Ahmad R, Budnik B. A review of the current state of single-cell proteomics and future perspective. Anal Bioanal Chem 2023; 415:6889-6899. [PMID: 37285026 PMCID: PMC10632274 DOI: 10.1007/s00216-023-04759-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
Single-cell methodologies and technologies have started a revolution in biology which until recently has primarily been limited to deep sequencing and imaging modalities. With the advent and subsequent torrid development of single-cell proteomics over the last 5 years, despite the fact that proteins cannot be amplified like transcripts, it has now become abundantly clear that it is a worthy complement to single-cell transcriptomics. In this review, we engage in an assessment of the current state of the art of single-cell proteomics including workflow, sample preparation techniques, instrumentation, and biological applications. We investigate the challenges associated with working with very small sample volumes and the acute need for robust statistical methods for data interpretation. We delve into what we believe is a promising future for biological research at single-cell resolution and highlight some of the exciting discoveries that already have been made using single-cell proteomics, including the identification of rare cell types, characterization of cellular heterogeneity, and investigation of signaling pathways and disease mechanisms. Finally, we acknowledge that there are a number of outstanding and pressing problems that the scientific community vested in advancing this technology needs to resolve. Of prime importance is the need to set standards so that this technology becomes widely accessible allowing novel discoveries to be easily verifiable. We conclude with a plea to solve these problems rapidly so that single-cell proteomics can be part of a robust, high-throughput, and scalable single-cell multi-omics platform that can be ubiquitously applied to elucidating deep biological insights into the diagnosis and treatment of all diseases that afflict us.
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Affiliation(s)
- Rushdy Ahmad
- Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Bogdan Budnik
- Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA.
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34
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Montero-Calle A, Garranzo-Asensio M, Rejas-González R, Feliu J, Mendiola M, Peláez-García A, Barderas R. Benefits of FAIMS to Improve the Proteome Coverage of Deteriorated and/or Cross-Linked TMT 10-Plex FFPE Tissue and Plasma-Derived Exosomes Samples. Proteomes 2023; 11:35. [PMID: 37987315 PMCID: PMC10661291 DOI: 10.3390/proteomes11040035] [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: 07/19/2023] [Revised: 09/20/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023] Open
Abstract
The proteome characterization of complex, deteriorated, or cross-linked protein mixtures as paired clinical FFPE or exosome samples isolated from low plasma volumes (250 µL) might be a challenge. In this work, we aimed at investigating the benefits of FAIMS technology coupled to the Orbitrap Exploris 480 mass spectrometer for the TMT quantitative proteomics analyses of these complex samples in comparison to the analysis of protein extracts from cells, frozen tissue, and exosomes isolated from large volume plasma samples (3 mL). TMT experiments were performed using a two-hour gradient LC-MS/MS with or without FAIMS and two compensation voltages (CV = -45 and CV = -60). In the TMT experiments of cells, frozen tissue, or exosomes isolated from large plasma volumes (3 mL) with FAIMS, a limited increase in the number of identified and quantified proteins accompanied by a decrease in the number of peptides identified and quantified was observed. However, we demonstrated here a noticeable improvement (>100%) in the number of peptide and protein identifications and quantifications for the plasma exosomes isolated from low plasma volumes (250 µL) and FFPE tissue samples in TMT experiments with FAIMS in comparison to the LC-MS/MS analysis without FAIMS. Our results highlight the potential of mass spectrometry analyses with FAIMS to increase the depth into the proteome of complex samples derived from deteriorated, cross-linked samples and/or those where the material was scarce, such as FFPE and plasma-derived exosomes from low plasma volumes (250 µL), which might aid in the characterization of their proteome and proteoforms and in the identification of dysregulated proteins that could be used as biomarkers.
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Affiliation(s)
- Ana Montero-Calle
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.G.-A.); (R.R.-G.)
| | - María Garranzo-Asensio
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.G.-A.); (R.R.-G.)
| | - Raquel Rejas-González
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.G.-A.); (R.R.-G.)
| | - Jaime Feliu
- Translational Oncology Group, La Paz University Hospital (IdiPAZ), 28046 Madrid, Spain;
- Center for Biomedical Research in the Cancer Network (CIBERONC), Instituto de Salud Carlos III, 28046 Madrid, Spain;
| | - Marta Mendiola
- Center for Biomedical Research in the Cancer Network (CIBERONC), Instituto de Salud Carlos III, 28046 Madrid, Spain;
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), 28046 Madrid, Spain;
| | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), 28046 Madrid, Spain;
| | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.G.-A.); (R.R.-G.)
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Dowling P, Swandulla D, Ohlendieck K. Cellular pathogenesis of Duchenne muscular dystrophy: progressive myofibre degeneration, chronic inflammation, reactive myofibrosis and satellite cell dysfunction. Eur J Transl Myol 2023; 33:11856. [PMID: 37846661 PMCID: PMC10811648 DOI: 10.4081/ejtm.2023.11856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023] Open
Abstract
Duchenne muscular dystrophy is a highly progressive muscle wasting disease of early childhood and characterized by complex pathophysiological and histopathological changes in the voluntary contractile system, including myonecrosis, chronic inflammation, fat substitution and reactive myofibrosis. The continued loss of functional myofibres and replacement with non-contractile cells, as well as extensive tissue scarring and decline in tissue elasticity, leads to severe skeletal muscle weakness. In addition, dystrophic muscles exhibit a greatly diminished regenerative capacity to counteract the ongoing process of fibre degeneration. In normal muscle tissues, an abundant stem cell pool consisting of satellite cells that are localized between the sarcolemma and basal lamina, provides a rich source for the production of activated myogenic progenitor cells that are involved in efficient myofibre repair and tissue regeneration. Interestingly, the self-renewal of satellite cells for maintaining an essential pool of stem cells in matured skeletal muscles is increased in dystrophin-deficient fibres. However, satellite cell hyperplasia does not result in efficient recovery of dystrophic muscles due to impaired asymmetric cell divisions. The lack of expression of the full-length dystrophin isoform Dp427-M, which is due to primary defects in the DMD gene, appears to affect key regulators of satellite cell polarity causing a reduced differentiation of myogenic progenitors, which are essential for myofibre regeneration. This review outlines the complexity of dystrophinopathy and describes the importance of the pathophysiological role of satellite cell dysfunction. A brief discussion of the bioanalytical usefulness of single cell proteomics for future studies of satellite cell biology is provided.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
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Thielert M, Itang ECM, Ammar C, Rosenberger FA, Bludau I, Schweizer L, Nordmann TM, Skowronek P, Wahle M, Zeng W, Zhou X, Brunner A, Richter S, Levesque MP, Theis FJ, Steger M, Mann M. Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Mol Syst Biol 2023; 19:e11503. [PMID: 37602975 PMCID: PMC10495816 DOI: 10.15252/msb.202211503] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023] Open
Abstract
Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.
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Affiliation(s)
- Marvin Thielert
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Ericka CM Itang
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Constantin Ammar
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Florian A Rosenberger
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Isabell Bludau
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Lisa Schweizer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Thierry M Nordmann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Patricia Skowronek
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Maria Wahle
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Wen‐Feng Zeng
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Xie‐Xuan Zhou
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Andreas‐David Brunner
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery SciencesBiberach an der RissGermany
| | - Sabrina Richter
- Helmholtz Zentrum München – German Research Center for Environmental HealthInstitute of Computational BiologyNeuherbergGermany
- TUM School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany
| | - Mitchell P Levesque
- Department of DermatologyUniversity of Zurich, University of Zurich HospitalZurichSwitzerland
| | - Fabian J Theis
- Helmholtz Zentrum München – German Research Center for Environmental HealthInstitute of Computational BiologyNeuherbergGermany
- TUM School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany
| | - Martin Steger
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- New address: NEOsphere Biotechnologies GmbHPlaneggGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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Abdelkader Y, Perez-Davalos L, LeDuc R, Zahedi RP, Labouta HI. Omics approaches for the assessment of biological responses to nanoparticles. Adv Drug Deliv Rev 2023; 200:114992. [PMID: 37414362 DOI: 10.1016/j.addr.2023.114992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.
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Affiliation(s)
- Yasmin Abdelkader
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St., Cairo 12622, Egypt
| | - Luis Perez-Davalos
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada
| | - Richard LeDuc
- Children's Hospital Research Institute of Manitoba, 513 - 715 McDermot Av. W, Winnipeg, Manitoba R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada; Department of Internal Medicine, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; CancerCare Manitoba Research Institute, 675 McDermot Av., Manitoba R3E 0V9, Canada
| | - Hagar I Labouta
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario M5S 3M2, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada; Faculty of Pharmacy, Alexandria University, 1 Khartoum Square, Azarita, Alexandria, Egypt, 21521.
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Meah A, Vedarethinam V, Bronstein R, Gujarati N, Jain T, Mallipattu SK, Li Y, Wang J. Single-Cell Spatial MIST for Versatile, Scalable Detection of Protein Markers. BIOSENSORS 2023; 13:852. [PMID: 37754086 PMCID: PMC10526469 DOI: 10.3390/bios13090852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
High-multiplex detection of protein biomarkers across tissue regions has been an attractive spatial biology approach due to significant advantages over traditional immunohistochemistry (IHC) methods. Different from most methods, spatial multiplex in situ tagging (MIST) transfers the spatial protein expression information to an ultrahigh-density, large-scale MIST array. This technique has been optimized to reach single-cell resolution by adoption of smaller array units and 30% 8-arm PEG polymer as transfer medium. Tissue cell nuclei stained with lamin B have been clearly visualized on the MIST arrays and are colocalized with detection of nine mouse brain markers. Pseudocells defined at 10 μm in size have been used to fully profile tissue regions including cells and the intercellular space. We showcased the versatility of our technology by successfully detecting 20 marker proteins in kidney samples with the addition of five minutes atop the duration of standard immunohistochemistry protocols. Spatial MIST is amenable to iterative staining and detection on the same tissue samples. When 25 proteins were co-detected on 1 mouse brain section for each round and 5 rounds were executed, an ultrahigh multiplexity of 125 proteins was obtained for each pseudocell. With its unique abilities, this single-cell spatial MIST technology has the potential to become an important method in advanced diagnosis of complex diseases.
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Affiliation(s)
- Arafat Meah
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Vadanasundari Vedarethinam
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Robert Bronstein
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
| | - Nehaben Gujarati
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
| | - Tanya Jain
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA
| | - Sandeep K. Mallipattu
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
- Renal Section, Northport VA Medical Center, Northport, NY 11768, USA
| | - Yueming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA
- Programs of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
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Zhang H, Liu Y, Fields L, Shi X, Huang P, Lu H, Schneider AJ, Tang X, Puglielli L, Welham NV, Li L. Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging. Nat Commun 2023; 14:5185. [PMID: 37626051 PMCID: PMC10457347 DOI: 10.1038/s41467-023-40512-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Single-cell (SC) analysis provides unique insight into individual cell dynamics and cell-to-cell heterogeneity. Here, we utilize trapped ion mobility separation coupled with dual-polarity ionization mass spectrometry imaging (MSI) to enable high-throughput in situ profiling of the SC lipidome. Multimodal SC imaging, in which dual-polarity-mode MSI is used to perform serial data acquisition runs on individual cells, significantly enhanced SC lipidome coverage. High-spatial resolution SC-MSI identifies both inter- and intracellular lipid heterogeneity; this heterogeneity is further explicated by Uniform Manifold Approximation and Projection and machine learning-driven classifications. We characterize SC lipidome alteration in response to stearoyl-CoA desaturase 1 inhibition and, additionally, identify cell-layer specific lipid distribution patterns in mouse cerebellar cortex. This integrated multimodal SC-MSI technology enables high-resolution spatial mapping of intercellular and cell-to-cell lipidome heterogeneity, SC lipidome remodeling induced by pharmacological intervention, and region-specific lipid diversity within tissue.
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Affiliation(s)
- Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Yuan Liu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53792, USA
| | - Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Andrew J Schneider
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Xindi Tang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Nathan V Welham
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53792, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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40
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Truong T, Webber KGI, Madisyn Johnston S, Boekweg H, Lindgren CM, Liang Y, Nydegger A, Xie X, Tsang TM, Jayatunge DADN, Andersen JL, Payne SH, Kelly RT. Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics. Angew Chem Int Ed Engl 2023; 62:e202303415. [PMID: 37380610 PMCID: PMC10529037 DOI: 10.1002/anie.202303415] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
We combined efficient sample preparation and ultra-low-flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in rapid label-free analyses. WWA employs large isolation windows to intentionally co-isolate and co-fragment adjacent precursors along with the selected precursor. Optimized WWA increased the number of MS2-identified proteins by ≈40 % relative to standard data-dependent acquisition. For a 40-min LC gradient operated at ≈15 nL/min, we identified an average of 3,524 proteins per single-cell-sized aliquot of protein digest. Reducing the active gradient to 20 min resulted in a modest 10 % decrease in proteome coverage. Using this platform, we compared protein expression between single HeLa cells having an essential autophagy gene, atg9a, knocked out, with their isogenic WT parental line. Similar proteome coverage was observed, and 268 proteins were significantly up- or downregulated. Protein upregulation primarily related to innate immunity, vesicle trafficking and protein degradation.
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Affiliation(s)
- Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Hannah Boekweg
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Caleb M Lindgren
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Alissia Nydegger
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Xiaofeng Xie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Tsz-Ming Tsang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - D A Dasun N Jayatunge
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Joshua L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
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Johnston SM, Webber KGI, Xie X, Truong T, Nydegger A, Lin HJL, Nwosu A, Zhu Y, Kelly RT. Rapid, One-Step Sample Processing for Label-Free Single-Cell Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1701-1707. [PMID: 37410391 PMCID: PMC11017373 DOI: 10.1021/jasms.3c00159] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Sample preparation for single-cell proteomics is generally performed in a one-pot workflow with multiple dispensing and incubation steps. These hours-long processes can be labor intensive and lead to long sample-to-answer times. Here we report a sample preparation method that achieves cell lysis, protein denaturation, and digestion in 1 h using commercially available high-temperature-stabilized proteases with a single reagent dispensing step. Four different one-step reagent compositions were evaluated, and the mixture providing the highest proteome coverage was compared to the previously employed multistep workflow. The one-step preparation increases proteome coverage relative to the previous multistep workflow while minimizing labor input and the possibility of human error. We also compared sample recovery between previously used microfabricated glass nanowell chips and injection-molded polypropylene chips and found the polypropylene provided improved proteome coverage. Combined, the one-step sample preparation and the polypropylene substrates enabled the identification of an average of nearly 2400 proteins per cell using a standard data-dependent workflow with Orbitrap mass spectrometers. These advances greatly simplify sample preparation for single-cell proteomics and broaden accessibility with no compromise in terms of proteome coverage.
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Affiliation(s)
- S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Xiaofeng Xie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Alissia Nydegger
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Hsien-Jung L Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Andikan Nwosu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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Kong L, Li F, Fang W, Du Z, Wang G, Zhang Y, Ge WP, Zhang W, Qin W. Sensitive N-Glycopeptide Profiling of Single and Rare Cells Using an Isobaric Labeling Strategy without Enrichment. Anal Chem 2023; 95:11326-11334. [PMID: 37409763 DOI: 10.1021/acs.analchem.3c01392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Single-cell omics is critical in revealing population heterogeneity, discovering unique features of individual cells, and identifying minority subpopulations of interest. As one of the major post-translational modifications, protein N-glycosylation plays crucial roles in various important biological processes. Elucidation of the variation in N-glycosylation patterns at single-cell resolution may largely facilitate the understanding of their key roles in the tumor microenvironment and immune therapy. However, comprehensive N-glycoproteome profiling for single cells has not been achieved due to the extremely limited sample amount and incompatibility with the available enrichment strategies. Here, we have developed an isobaric labeling-based carrier strategy for highly sensitive intact N-glycopeptide profiling for single cells or a small number of rare cells without enrichment. Isobaric labeling has unique multiplexing properties, by which the "total" signal from all channels triggers MS/MS fragmentation for N-glycopeptide identification, while the reporter ions provide quantitative information. In our strategy, a carrier channel using N-glycopeptides obtained from bulk-cell samples significantly improved the "total" signal of N-glycopeptides and, therefore, promoted the first quantitative analysis of averagely 260 N-glycopeptides from single HeLa cells. We further applied this strategy to study the regional heterogeneity of N-glycosylation of microglia in mouse brain and discovered region-specific N-glycoproteome patterns and cell subtypes. In conclusion, the glycocarrier strategy provides an attractive solution for sensitive and quantitative N-glycopeptide profiling of single/rare cells that cannot be enriched by traditional workflows.
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Affiliation(s)
- Linlin Kong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Fengzhi Li
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Wei Fang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Zhuokun Du
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Guibin Wang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yangjun Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Woo-Ping Ge
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Wanjun Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
- College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
- College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
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43
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Mun DG, Bhat FA, Ding H, Madden BJ, Natesampillai S, Badley AD, Johnson KL, Kelly RT, Pandey A. Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments. Analyst 2023; 148:3466-3475. [PMID: 37395315 PMCID: PMC10370902 DOI: 10.1039/d3an00080j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/10/2023] [Indexed: 07/04/2023]
Abstract
Although single cell RNA-seq has had a tremendous impact on biological research, a corresponding technology for unbiased mass spectrometric analysis of single cells has only recently become available. Significant technological breakthroughs including miniaturized sample handling have enabled proteome profiling of single cells. Furthermore, trapped ion mobility spectrometry (TIMS) in combination with parallel accumulation-serial fragmentation operated in data-dependent acquisition mode (DDA-PASEF) allowed improved proteome coverage from low-input samples. It has been demonstrated that modulating the ion flux in TIMS affects the overall performance of proteome profiling. However, the effect of TIMS settings on the analysis of low-input samples has been less investigated. Thus, we sought to optimize the conditions of TIMS with regard to ion accumulation/ramp times and ion mobility range for low-input samples. We observed that an ion accumulation time of 180 ms and monitoring a narrower ion mobility range from 0.7 to 1.3 V s cm-2 resulted in a substantial gain in the depth of proteome coverage and in detecting proteins with low abundance. We used these optimized conditions for proteome profiling of sorted human primary T cells, which yielded an average of 365, 804, 1116, and 1651 proteins from single, five, ten, and forty T cells, respectively. Notably, we demonstrated that the depth of proteome coverage from a low number of cells was sufficient to delineate several essential metabolic pathways and the T cell receptor signaling pathway. Finally, we showed the feasibility of detecting post-translational modifications including phosphorylation and acetylation from single cells. We believe that such an approach could be applied to label-free analysis of single cells obtained from clinically relevant samples.
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Affiliation(s)
- Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | - Firdous A Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | - Husheng Ding
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | | | | | - Andrew D Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
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44
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Kim JH, Afridi R, Lee WH, Suk K. Analyzing the glial proteome in Alzheimer's disease. Expert Rev Proteomics 2023; 20:197-209. [PMID: 37724426 DOI: 10.1080/14789450.2023.2260955] [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: 06/09/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence indicates that dysfunction of glial cells, including astrocytes, microglia, and oligodendrocytes, may contribute to the development and progression of AD. Large-scale analysis of glial proteins sheds light on their roles in cellular processes and diseases. In AD, glial proteomics has been utilized to understand glia-based pathophysiology and identify potential biomarkers and therapeutic targets. AREA COVERED In this review, we provide an updated overview of proteomic analysis of glia in the context of AD. Additionally, we discuss current challenges in the field, involving glial complexity and heterogeneity, and describe some cutting-edge proteomic technologies to address them. EXPERT OPINION Unbiased comprehensive analysis of glial proteomes aids our understanding of the molecular and cellular mechanisms of AD pathogenesis. These investigations highlight the crucial role of glial cells and provide novel insights into the mechanisms of AD pathology. A deeper understanding of the AD-related glial proteome could offer a repertoire of potential biomarkers and therapeutics. Further technical advancement of glial proteomics will enable us to identify proteins within individual cells and specific cell types, thus significantly enhancing our comprehension of AD pathogenesis.
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Affiliation(s)
- Jong-Heon Kim
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Ruqayya Afridi
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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45
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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: 14] [Impact Index Per Article: 14.0] [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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46
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Hu M, Zhang Y, Yuan Y, Ma W, Zheng Y, Gu Q, Xie XS. Correlated Protein Modules Revealing Functional Coordination of Interacting Proteins Are Detected by Single-Cell Proteomics. J Phys Chem B 2023. [PMID: 37368753 DOI: 10.1021/acs.jpcb.3c00014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Single-cell proteomics has attracted a lot of attention in recent years because it offers more functional relevance than single-cell transcriptomics. However, most work to date has focused on cell typing, which has been widely accomplished by single-cell transcriptomics. Here we report the use of single-cell proteomics to measure the correlation between the translational levels of a pair of proteins in a single mammalian cell. In measuring pairwise correlations among ∼1000 proteins in a population of homogeneous K562 cells under a steady-state condition, we observed multiple correlated protein modules (CPMs), each containing a group of highly positively correlated proteins that are functionally interacting and collectively involved in certain biological functions, such as protein synthesis and oxidative phosphorylation. Some CPMs are shared across different cell types while others are cell-type specific. Widely studied in omics analyses, pairwise correlations are often measured by introducing perturbations into bulk samples. However, some correlations of gene or protein expression under the steady-state condition would be masked by perturbation. The single-cell correlations probed in our experiment reflect intrinsic steady-state fluctuations in the absence of perturbation. We note that observed correlations between proteins are experimentally more distinct and functionally more relevant than those between corresponding mRNAs measured in single-cell transcriptomics. By virtue of single-cell proteomics, functional coordination of proteins is manifested through CPMs.
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Affiliation(s)
- Mo Hu
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- Changping Laboratory, Beijing 102206, China
| | - Yutong Zhang
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yuan Yuan
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenping Ma
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yinghui Zheng
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | | | - X Sunney Xie
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- Changping Laboratory, Beijing 102206, China
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47
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Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler AR, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. CELL REPORTS METHODS 2023; 3:100511. [PMID: 37426761 PMCID: PMC10326451 DOI: 10.1016/j.crmeth.2023.100511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.
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Affiliation(s)
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Zhaoguan Wu
- CHU Sainte Justine Research Center, Montreal, QC, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Department of Chemistry, University of Montreal, Montreal, QC, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Etienne Caron
- CHU Sainte Justine Research Center, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, University of Montreal, Montreal, QC, Canada
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48
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Park N, Lee H, Kwon Y, Ju S, Lee S, Yoo S, Park KS, Lee C. One-STAGE Tip Method for TMT-Based Proteomic Analysis of a Minimal Amount of Cells. ACS OMEGA 2023; 8:19741-19751. [PMID: 37305273 PMCID: PMC10249390 DOI: 10.1021/acsomega.3c01392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS)-based profiling of proteomes with isobaric tag labeling from low-quantity biological and clinical samples, including needle-core biopsies and laser capture microdissection, has been challenging due to the limited amount and sample loss during preparation. To address this problem, we developed OnM (On-Column from Myers et al. and mPOP)-modified on-column method combining freeze-thaw lysis of mPOP with isobaric tag labeling of On-Column method to minimize sample loss. OnM is a method that processes the sample in one-STAGE tip from cell lysis to tandem mass tag (TMT) labeling without any transfer of the sample. In terms of protein coverage, cellular components, and TMT labeling efficiency, the modified On-Column (or OnM) displayed similar performance to the results from Myers et al. To evaluate the lower-limit processing capability of OnM, we utilized OnM for multiplexing and were able to quantify 301 proteins in a TMT 9-plex with 50 cells per channel. We optimized the method as low as 5 cells per channel in which we identified 51 quantifiable proteins. OnM method is a low-input proteomics method widely applicable and capable of identifying and quantifying proteomes from limited samples, with tools that are readily available in a majority of proteomic laboratories.
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Affiliation(s)
- Narae Park
- Chemical
& Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- KHU-KIST
Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Hankyul Lee
- Chemical
& Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- KHU-KIST
Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Yumi Kwon
- Chemical
& Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Shinyeong Ju
- Chemical
& Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seonjeong Lee
- Chemical
& Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division
of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Seongjin Yoo
- Chemical
& Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division
of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Kang-Sik Park
- KHU-KIST
Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
- Department
of Physiology, School of Medicine, Kyung
Hee University, Seoul 02447, Korea
| | - Cheolju Lee
- Chemical
& Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division
of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
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Ai L, Binek A, Kreimer S, Ayres M, Stotland A, Van Eyk JE. High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing. J Proteome Res 2023; 22:2124-2130. [PMID: 37040897 PMCID: PMC10243111 DOI: 10.1021/acs.jproteome.3c00027] [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: 01/12/2023] [Indexed: 04/13/2023]
Abstract
Heart tissue sample preparation for mass spectrometry (MS) analysis that includes prefractionation reduces the cellular protein dynamic range and increases the relative abundance of nonsarcomeric proteins. We previously described "IN-Sequence" (IN-Seq) where heart tissue lysate is sequentially partitioned into three subcellular fractions to increase the proteome coverage more than a single direct tissue analysis by mass spectrometry. Here, we report an adaptation of the high-field asymmetric ion mobility spectrometry (FAIMS) coupled to mass spectrometry, and the establishment of a simple one step sample preparation coupled with gas-phase fractionation. The FAIMS approach substantially reduces manual sample handling, significantly shortens the MS instrument processing time, and produces unique protein identification and quantification approximating the commonly used IN-Seq method in less time.
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Affiliation(s)
- Lizhuo Ai
- Department
of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Simion Kreimer
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Matthew Ayres
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandr Stotland
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- Department
of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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50
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Lohani V, A.R A, Kundu S, Akhter MDQ, Bag S. Single-Cell Proteomics with Spatial Attributes: Tools and Techniques. ACS OMEGA 2023; 8:17499-17510. [PMID: 37251119 PMCID: PMC10210017 DOI: 10.1021/acsomega.3c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/12/2023] [Indexed: 05/31/2023]
Abstract
Now-a-days, the single-cell proteomics (SCP) concept is attracting interest, especially in clinical research, because it can identify the proteomic signature specific to diseased cells. This information is very essential when dealing with the progression of certain diseases, such as cancer, diabetes, Alzheimer's, etc. One of the major drawbacks of conventional destructive proteomics is that it gives an average idea about the protein expression profile in the disease condition. During the extraction of the protein from a biopsy or blood sample, proteins may come from both diseased cells and adjacent normal cells or any other cells from the disease environment. Again, SCP along with spatial attributes is utilized to learn about the heterogeneous function of a single protein. Before performing SCP, it is necessary to isolate single cells. This can be done by various techniques, including fluorescence-activated cell sorting (FACS), magnetic-activated cell sorting (MACS), laser capture microdissection (LCM), microfluidics, manual cell picking/micromanipulation, etc. Among the different approaches for proteomics, mass spectrometry-based proteomics tools are widely used for their high resolution as well as sensitivity. This Review mainly focuses on the mass spectrometry-based approaches for the study of single-cell proteomics.
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Affiliation(s)
- Vartika Lohani
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- PG Scholar, Department of Pharmacy, Banasthali
Vidyapith, Jaipur, Rajasthan 302001, India
| | - Akhiya A.R
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- PG Scholar, Department of Computational
Biology and Bioinformatics, University of
Kerala, Thiruvananthapuram, Kerala 695034, India
| | - Soumen Kundu
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - MD Quasid Akhter
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
| | - Swarnendu Bag
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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