1
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Li J, Huang L, Guo Y, Cupp-Sutton KA, Wu S. An automated spray-capillary platform for the microsampling and CE-MS analysis of picoliter- and nanoliter-volume samples. Anal Bioanal Chem 2023; 415:6961-6973. [PMID: 37581707 PMCID: PMC10843549 DOI: 10.1007/s00216-023-04870-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 08/16/2023]
Abstract
Capillary electrophoresis mass spectrometry (CE-MS) is an emerging analytical tool for microscale biological sample analysis that offers high separation resolution, low detection limit, and low sample consumption. We recently developed a novel microsampling device, "spray-capillary," for quantitative low-volume sample extraction (as low as 15 pL/s) and online CE-MS analysis. This platform can efficiently analyze picoliter samples (e.g., single cells) with minimal sample loss and no additional offline sample-handling steps. However, our original spray-capillary-based experiments required manual manipulation of the sample inlet for sample collection and separation, which is time consuming and requires proficiency in device handling. To optimize the performance of spray-capillary CE-MS analysis, we developed an automated platform for robust, high-throughput analysis of picoliter samples using a commercially available CE autosampler. Our results demonstrated high reproducibility among 50 continuous runs using the standard peptide angiotensin II (Ang II), with an RSD of 14.70% and 0.62% with respect to intensity and elution time, respectively. We also analyzed Ang II using varying injection times to evaluate the capability of the spray-capillary to perform quantitative sampling and found high linearity for peptide intensity with respect to injection time (R2 > 0.99). These results demonstrate the capability of the spray-capillary sampling platform for high-throughput quantitative analysis of low-volume, low-complexity samples using pressure elution (e.g., direct injection). To further evaluate and optimize the automated spray-capillary platform to analyze complex biological samples, we performed online CE-MS analysis on Escherichia coli lysate digest spiked with Ang II using varying injection times. We maintained high linearity of intensity with respect to injection time for Ang II and E. coli peptides (R2 > 0.97 in all cases). Furthermore, we observed good CE separation and high reproducibility between automated runs. Overall, we demonstrated that the automated spray-capillary CE-MS platform can efficiently and reproducibly sample picoliter and nanoliter biological samples for high-throughput proteomics analysis.
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Affiliation(s)
- Jiaxue Li
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA
| | - Lushuang Huang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA
| | - Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA.
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA.
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2
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Tan G, Wolski WE, Kummer S, Hofstetter M, Theocharides APA, Manz MG, Aebersold R, Meier-Abt F. Proteomic identification of proliferation and progression markers in human polycythemia vera stem and progenitor cells. Blood Adv 2022; 6:3480-3493. [PMID: 35008095 PMCID: PMC9198936 DOI: 10.1182/bloodadvances.2021005344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/07/2021] [Indexed: 11/20/2022] Open
Abstract
Polycythemia vera (PV) is a stem cell disorder characterized by hyperproliferation of the myeloid lineages and the presence of an activating JAK2 mutation. To elucidate mechanisms controlling PV stem and progenitor cell biology, we applied a recently developed highly sensitive data-independent acquisition mass spectrometry workflow to purified hematopoietic stem and progenitor cell (HSPC) subpopulations of patients with chronic and progressed PV. We integrated proteomic data with genomic, transcriptomic, flow cytometry, and in vitro colony formation data. Comparative analyses revealed added information gained by proteomic compared with transcriptomic data in 30% of proteins with changed expression in PV patients. Upregulated biological pathways in hematopoietic stem and multipotent progenitor cells (HSC/MPPs) of PV included mammalian target of rapamycin (MTOR), STAT, and interferon signaling. We further identified a prominent reduction of clusterin (CLU) protein expression and a corresponding activation of nuclear factor-κB (NF-κB) signaling in HSC/MPPs of untreated PV patients compared with controls. Reversing the reduction of CLU and inhibiting NF-κB signaling decreased proliferation and differentiation of PV HSC/MPPs in vitro. Upon progression of PV, we identified upregulation of LGALS9 and SOCS2 protein expression in HSC/MPPs. Treatment of patients with hydroxyurea normalized the expression of CLU and NF-κB2 but not of LGALS9 and SOCS2. These findings expand the current understanding of the molecular pathophysiology underlying PV and provide new potential targets (CLU and NF-κB) for antiproliferative therapy in patients with PV.
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Affiliation(s)
- Ge Tan
- Functional Genomics Center Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Witold E. Wolski
- Functional Genomics Center Zurich, University and ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandra Kummer
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Mara Hofstetter
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Alexandre P. A. Theocharides
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Markus G. Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland; and
| | - Fabienne Meier-Abt
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, Schlieren (Zurich), Switzerland
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3
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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4
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Yang S, Xiong Y, Du Y, Wang YJ, Zhang L, Shen F, Liu YJ, Liu X, Yang P. Ultrasensitive Trace Sample Proteomics Unraveled the Protein Remodeling during Mesenchymal-Amoeboid Transition. Anal Chem 2021; 94:768-776. [PMID: 34928127 DOI: 10.1021/acs.analchem.1c03212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deep mining the proteome of trace biological samples is critical for biomedical applications. However, it remains a challenge due to the loss of analytes caused by current sample preparation procedures. To address this, we recently developed a single-pot and miniaturized in-solution digestion (SMID) method for minute sample handling with three streamlined steps and completed within 3 h. The SMID approach outperformed the traditional workflow in substantially saving time, reducing sample loss, and exhibiting extensive applicability for 10-100 000 cell analysis. This user-friendly and high-sensitivity strategy enables ∼5300 proteins and 53 000 peptides to be confidently identified within 1 h of mass spectrometry (MS) time from a small amount of 1000 HeLa cells. In addition, we accurately and robustly detected proteomes in 10 mouse oocytes with excellent reproducibility. We further adopted SMID for the proteome analysis in cell migration under confinement, which induced cells to undergo a mesenchymal-amoeboid transition (MAT). During the MAT, a systematic quantitative proteome map of 1000 HeLa cells was constructed with seven expression profile clusters, which illustrated the application of SMID and provided a fundamental resource to investigate the mechanism of MAT.
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Affiliation(s)
- Shuang Yang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yueting Xiong
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yang Du
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ya-Jun Wang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Fenglin Shen
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yan-Jun Liu
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaohui Liu
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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5
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Weke K, Singh A, Uwugiaren N, Alfaro JA, Wang T, Hupp TR, O'Neill JR, Vojtesek B, Goodlett DR, Williams SM, Zhou M, Kelly RT, Zhu Y, Dapic I. MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress. J Proteome Res 2021; 20:2195-2205. [PMID: 33491460 PMCID: PMC8155554 DOI: 10.1021/acs.jproteome.0c00629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Moving from macroscale
preparative systems in proteomics to micro-
and nanotechnologies offers researchers the ability to deeply profile
smaller numbers of cells that are more likely to be encountered in
clinical settings. Herein a recently developed microscale proteomic
method, microdroplet processing in one pot for trace samples (microPOTS),
was employed to identify proteomic changes in ∼200 Barrett’s
esophageal cells following physiologic and radiation stress exposure.
From this small population of cells, microPOTS confidently identified
>1500 protein groups, and achieved a high reproducibility with
a Pearson’s
correlation coefficient value of R > 0.9 and over
50% protein overlap from replicates. A Barrett’s cell line
model treated with either lithocholic acid (LCA) or X-ray had 21 (e.g.,
ASNS, RALY, FAM120A, UBE2M, IDH1, ESD) and 32 (e.g., GLUL, CALU, SH3BGRL3,
S100A9, FKBP3, AGR2) overexpressed proteins, respectively, compared
to the untreated set. These results demonstrate the ability of microPOTS
to routinely identify and quantify differentially expressed proteins
from limited numbers of cells.
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Affiliation(s)
- Kenneth Weke
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Ashita Singh
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K.,Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Naomi Uwugiaren
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Javier A Alfaro
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - Tongjie Wang
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - Ted R Hupp
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - J Robert O'Neill
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K.,Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, U.K
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - David R Goodlett
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC V8Z 7X8, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Irena Dapic
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
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6
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Lu X, Wang Z, Gao Y, Chen W, Wang L, Huang P, Gao W, Ke M, He A, Tian R. AutoProteome Chip System for Fully Automated and Integrated Proteomics Sample Preparation and Peptide Fractionation. Anal Chem 2020; 92:8893-8900. [DOI: 10.1021/acs.analchem.0c00752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xue Lu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhikun Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Gao
- Hochuen Medical Technology Co., Ltd., Shenzhen 518109, China
| | - Wendong Chen
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lingjue Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Peiwu Huang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Weina Gao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Mi Ke
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - An He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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7
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Amon S, Meier-Abt F, Gillet LC, Dimitrieva S, Theocharides APA, Manz MG, Aebersold R. Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry. Mol Cell Proteomics 2019; 18:1454-1467. [PMID: 30975897 PMCID: PMC6601215 DOI: 10.1074/mcp.tir119.001431] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Physiological processes in multicellular organisms depend on the function and interactions of specialized cell types operating in context. Some of these cell types are rare and thus obtainable only in minute quantities. For example, tissue-specific stem and progenitor cells are numerically scarce, but functionally highly relevant, and fulfill critical roles in development, tissue maintenance, and disease. Whereas low numbers of cells are routinely analyzed by genomics and transcriptomics, corresponding proteomic analyses have so far not been possible due to methodological limitations. Here we describe a sensitive and robust quantitative technique based on data-independent acquisition mass spectrometry. We quantified the proteome of sets of 25,000 human hematopoietic stem/multipotent progenitor cells (HSC/MPP) and three committed progenitor cell subpopulations of the myeloid differentiation pathway (common myeloid progenitors, megakaryocyte-erythrocyte progenitors, and granulocyte-macrophage progenitors), isolated by fluorescence-activated cell sorting from five healthy donors. On average, 5,851 protein groups were identified per sample. A subset of 4,131 stringently filtered protein groups was quantitatively compared across the 20 samples, defining unique signatures for each subpopulation. A comparison of proteomic and transcriptomic profiles indicated HSC/MPP-specific divergent regulation of biochemical functions such as telomerase maintenance and quiescence-inducing enzymes, including isocitrate dehydrogenases. These are essential for maintaining stemness and were detected at proteome, but not transcriptome, level. The method is equally applicable to almost any rare cell type, including healthy and cancer stem cells or physiologically and pathologically infiltrating cell populations. It thus provides essential new information toward the detailed biochemical understanding of cell development and functionality in health and disease.
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Affiliation(s)
- Sabine Amon
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Fabienne Meier-Abt
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland;; §Hematology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ludovic C Gillet
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Slavica Dimitrieva
- ¶Functional Genomics Center Zurich, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland
| | | | - Markus G Manz
- §Hematology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland;; ‖Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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8
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Xu K, Liang Y, Piehowski PD, Dou M, Schwarz KC, Zhao R, Sontag RL, Moore RJ, Zhu Y, Kelly RT. Benchtop-compatible sample processing workflow for proteome profiling of < 100 mammalian cells. Anal Bioanal Chem 2019; 411:4587-4596. [PMID: 30460388 PMCID: PMC6527493 DOI: 10.1007/s00216-018-1493-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022]
Abstract
Extending proteomics to smaller samples can enable the mapping of protein expression across tissues with high spatial resolution and can reveal sub-group heterogeneity. However, despite the continually improving sensitivity of LC-MS instrumentation, in-depth profiling of samples containing low-nanogram amounts of protein has remained challenging due to analyte losses incurred during preparation and analysis. To address this, we recently developed nanodroplet processing in one pot for trace samples (nanoPOTS), a robotic/microfluidic platform that generates ready-to-analyze peptides from cellular material in ~200 nL droplets with greatly reduced sample losses. In combination with ultrasensitive LC-MS, nanoPOTS has enabled >3000 proteins to be confidently identified from as few as 10 cultured human cells and ~700 proteins from single cells. However, the nanoPOTS platform requires a highly skilled operator and a costly in-house-built robotic nanopipetting instrument. In this work, we sought to evaluate the extent to which the benefits of nanodroplet processing could be preserved when upscaling reagent dispensing volumes by a factor of 10 to those addressable by commercial micropipette. We characterized the resulting platform, termed microdroplet processing in one pot for trace samples (μPOTS), for the analysis of as few as ~25 cultured HeLa cells (4 ng total protein) or 50 μm square mouse liver tissue thin sections and found that ~1800 and ~1200 unique proteins were respectively identified with high reproducibility. The reduced equipment requirements should facilitate broad dissemination of nanoproteomics workflows by obviating the need for a capital-intensive custom liquid handling system.
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Affiliation(s)
- Kerui Xu
- W.R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT, 84602, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Maowei Dou
- W.R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kaitlynn C Schwarz
- W.R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Rui Zhao
- W.R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Ryan L Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ying Zhu
- W.R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
| | - Ryan T Kelly
- W.R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT, 84602, USA.
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9
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10
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Li ZY, Huang M, Wang XK, Zhu Y, Li JS, Wong CCL, Fang Q. Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis. Anal Chem 2018; 90:5430-5438. [PMID: 29551058 DOI: 10.1021/acs.analchem.8b00661] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell proteomic analysis provides crucial information on cellular heterogeneity in biological systems. Herein, we describe a nanoliter-scale oil-air-droplet (OAD) chip for achieving multistep complex sample pretreatment and injection for single cell proteomic analysis in the shotgun mode. By using miniaturized stationary droplet microreaction and manipulation techniques, our system allows all sample pretreatment and injection procedures to be performed in a nanoliter-scale droplet with minimum sample loss and a high sample injection efficiency (>99%), thus substantially increasing the analytical sensitivity for single cell samples. We applied the present system in the proteomic analysis of 100 ± 10, 50 ± 5, 10, and 1 HeLa cell(s), and protein IDs of 1360, 612, 192, and 51 were identified, respectively. The OAD chip-based system was further applied in single mouse oocyte analysis, with 355 protein IDs identified at the single oocyte level, which demonstrated its special advantages of high enrichment of sequence coverage, hydrophobic proteins, and enzymatic digestion efficiency over the traditional in-tube system.
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Affiliation(s)
- Zi-Yi Li
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Min Huang
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Xiu-Kun Wang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science , Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Ying Zhu
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Jin-Song Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science , Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Catherine C L Wong
- Center for Precision Medicine Multi-Omics Research , Peking University Health Science Center , Beijing , 100191 , China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing , 100191 , China.,National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Qun Fang
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
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11
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Lee HJ, Kim HJ, Liebler DC. Efficient Microscale Basic Reverse Phase Peptide Fractionation for Global and Targeted Proteomics. J Proteome Res 2016; 15:2346-54. [PMID: 27255222 DOI: 10.1021/acs.jproteome.6b00102] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Analysis of small biological samples would benefit from an efficient microscale fractionation strategy that minimizes sample handling, transfer steps, and accompanying losses. Here we describe a microscale basic reverse phase liquid chromatographic (bRPLC) fractionation method that offers high reproducibility and efficiency for peptide mixtures from small (5-20 μg) samples. We applied our platform to detect differentially expressed proteins from lung tumor cell lines that are sensitive (11-18) and resistant (11-18R) to the tyrosine kinase inhibitor erlotinib. Label-free analyses of 5-20 μg samples yielded identifications of approximately 3,200 to 4,000 proteins with coefficients of variation of 1.9-8.9% in replicate analyses. iTRAQ analyses produced similar protein inventories. Label-free and iTRAQ analyses displayed high concordance in identifications of proteins differentially expressed in 11-18 and 11-18R cells. Micro-bRPLC fractionation of cell proteomes increased sensitivity by an average of 4.5-fold in targeted quantitation using parallel reaction monitoring for three representative receptor tyrosine kinases (EGFR, PDGFRA, and BMX), which are present at low abundance in 11-18 and 11-18R cells. These data illustrate the broad utility of micro-bRPLC fractionation for global and targeted proteomic analyses. Data are available through Proteome eXchange Accession PXD003604.
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Affiliation(s)
- Hyoung-Joo Lee
- Department of Biochemistry, Vanderbilt University School of Medicine , 607 Light Hall, 2215 Garland Avenue, Nashville, Tennessee 37232-0146, United States
| | - Hye-Jung Kim
- Department of Biochemistry, Vanderbilt University School of Medicine , 607 Light Hall, 2215 Garland Avenue, Nashville, Tennessee 37232-0146, United States
| | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University School of Medicine , 607 Light Hall, 2215 Garland Avenue, Nashville, Tennessee 37232-0146, United States
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12
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Chen W, Wang S, Adhikari S, Deng Z, Wang L, Chen L, Ke M, Yang P, Tian R. Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling. Anal Chem 2016; 88:4864-71. [PMID: 27062885 DOI: 10.1021/acs.analchem.6b00631] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Great efforts have been taken for developing high-sensitive mass spectrometry (MS)-based proteomic technologies, among which sample preparation is one of the major focus. Here, a simple and integrated spintip-based proteomics technology (SISPROT) consisting of strong cation exchange beads and C18 disk in one pipet tip was developed. Both proteomics sample preparation steps, including protein preconcentration, reduction, alkylation, and digestion, and reversed phase (RP)-based desalting and high-pH RP-based peptide fractionation can be achieved in a fully integrated manner for the first time. This easy-to-use technology achieved high sensitivity with negligible sample loss. Proteomic analysis of 2000 HEK 293 cells readily identified 1270 proteins within 1.4 h of MS time, while 7826 proteins were identified when 100000 cells were processed and analyzed within only 22 h of MS time. More importantly, the SISPROT can be easily multiplexed on a standard centrifuge with good reproducibility (Pearson correlation coefficient > 0.98) for both single-shot analysis and deep proteome profiling with five-step high-pH RP fractionation. The SISPROT was exemplified by the triplicate analysis of 100000 stem cells from human exfoliated deciduous teeth (SHED). This led to the identification of 9078 proteins containing 3771 annotated membrane proteins, which was the largest proteome data set for dental stem cells reported to date. We expect that the SISPROT will be well suited for deep proteome profiling for fewer than 100000 cells and applied for translational studies where multiplexed technology with good label-free quantification precision is required.
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Affiliation(s)
- Wendong Chen
- Department of Chemistry, Fudan University , Shanghai 200433, China
| | - Shuai Wang
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | - Zuhui Deng
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | | | | | - Pengyuan Yang
- Department of Chemistry, Fudan University , Shanghai 200433, China
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13
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Asano H, Shiraishi Y. Development of paper-based microfluidic analytical device for iron assay using photomask printed with 3D printer for fabrication of hydrophilic and hydrophobic zones on paper by photolithography. Anal Chim Acta 2015; 883:55-60. [DOI: 10.1016/j.aca.2015.04.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 03/23/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
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14
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Li S, Plouffe BD, Belov AM, Ray S, Wang X, Murthy SK, Karger BL, Ivanov AR. An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood. Mol Cell Proteomics 2015; 14:1672-83. [PMID: 25755294 DOI: 10.1074/mcp.m114.045724] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 12/29/2022] Open
Abstract
Isolation and molecular characterization of rare cells (e.g. circulating tumor and stem cells) within biological fluids and tissues has significant potential in clinical diagnostics and personalized medicine. The present work describes an integrated platform of sample procurement, preparation, and analysis for deep proteomic profiling of rare cells in blood. Microfluidic magnetophoretic isolation of target cells spiked into 1 ml of blood at the level of 1000-2000 cells/ml, followed by focused acoustics-assisted sample preparation has been coupled with one-dimensional PLOT-LC-MS methodology. The resulting zeptomole detection sensitivity enabled identification of ∼4000 proteins with injection of the equivalent of only 100-200 cells per analysis. The characterization of rare cells in limited volumes of physiological fluids is shown by the isolation and quantitative proteomic profiling of first MCF-7 cells spiked into whole blood as a model system and then two CD133+ endothelial progenitor and hematopoietic cells in whole blood from volunteers.
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Affiliation(s)
- Siyang Li
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Brian D Plouffe
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; ¶Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Arseniy M Belov
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Somak Ray
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts
| | - Xianzhe Wang
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Shashi K Murthy
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; ¶Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Barry L Karger
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Alexander R Ivanov
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
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15
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Jalali-Heravi M, Arrastia M, Gomez FA. How Can Chemometrics Improve Microfluidic Research? Anal Chem 2015; 87:3544-55. [DOI: 10.1021/ac504863y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mehdi Jalali-Heravi
- Department
of Chemistry and
Biochemistry, California State University, Los Angeles, 5151 State
University Drive, Los Angeles, California 90032-8202, United States
| | - Mary Arrastia
- Department
of Chemistry and
Biochemistry, California State University, Los Angeles, 5151 State
University Drive, Los Angeles, California 90032-8202, United States
| | - Frank A. Gomez
- Department
of Chemistry and
Biochemistry, California State University, Los Angeles, 5151 State
University Drive, Los Angeles, California 90032-8202, United States
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16
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Parker SJ, Raedschelders K, Van Eyk JE. Emerging proteomic technologies for elucidating context-dependent cellular signaling events: A big challenge of tiny proportions. Proteomics 2015; 15:1486-502. [PMID: 25545106 DOI: 10.1002/pmic.201400448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/31/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Aberrant cell signaling events either drive or compensate for nearly all pathologies. A thorough description and quantification of maladaptive signaling flux in disease is a critical step in drug development, and complex proteomic approaches can provide valuable mechanistic insights. Traditional proteomics-based signaling analyses rely heavily on in vitro cellular monoculture. The characterization of these simplified systems generates a rich understanding of the basic components and complex interactions of many signaling networks, but they cannot capture the full complexity of the microenvironments in which pathologies are ultimately made manifest. Unfortunately, techniques that can directly interrogate signaling in situ often yield mass-limited starting materials that are incompatible with traditional proteomics workflows. This review provides an overview of established and emerging techniques that are applicable to context-dependent proteomics. Analytical approaches are illustrated through recent proteomics-based studies in which selective sample acquisition strategies preserve context-dependent information, and where the challenge of minimal starting material is met by optimized sensitivity and coverage. This review is organized into three major technological themes: (i) LC methods in line with MS; (ii) antibody-based approaches; (iii) MS imaging with a discussion of data integration and systems modeling. Finally, we conclude with future perspectives and implications of context-dependent proteomics.
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Affiliation(s)
- Sarah J Parker
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA; Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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