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Influence of different sample preparation strategies on hypothesis-driven shotgun proteomic analysis of human saliva. OPEN CHEM 2022. [DOI: 10.1515/chem-2022-0216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Abstract
This research aimed to find an efficient and repeatable bottom-up proteolytic strategy to process the unstimulated human saliva. The focus is on monitoring immune system activation via the cytokine and interleukin signaling pathways. Carbohydrate metabolism is also being studied as a possible trigger of inflammation and joint damage in the context of the diagnostic procedure of temporomandibular joint disorder. The preparation of clean peptide mixtures for liquid chromatography–mass spectrometry analysis was performed considering different aspects of sample preparation: the filter-aided sample preparation (FASP) with different loadings of salivary proteins, the unfractionated saliva, amylase-depleted, and amylase-enriched salivary fractions. To optimize the efficiency of the FASP method, the protocols with the digestion in the presence of 80% acetonitrile and one-step digestion in the presence of 80% acetonitrile were used, omitting protein reduction and alkylation. The digestion procedures were repeated in the standard in-solution mode. Alternatively, the temperature of 24 and 37°C was examined during the trypsin digestion. DyNet analysis of the hierarchical networks of Gene Ontology terms corresponding to each sample preparation method for the bottom-up assay revealed the wide variability in protein properties. The method can easily be tailored to the specific samples and groups of proteins to be examined.
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Shao X, Wang X, Guan S, Lin H, Yan G, Gao M, Deng C, Zhang X. Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling. Anal Chem 2018; 90:14003-14010. [PMID: 30375851 DOI: 10.1021/acs.analchem.8b03692] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In our previous work, we have demonstrated an integrated proteome analysis device (iPAD-100) to analyze proteomes from 100 cells. (1) In this work, for the first time, a novel integrated device for single-cell analysis (iPAD-1) was developed to profile proteins in a single cell within 1 h. In the iPAD-1, a selected single cell was directly sucked into a 22 μm i.d. capillary. Then the cell lysis and protein digestion were simultaneously accomplished in the capillary in a 2 nL volume, which could prevent protein loss and excessive dilution. Digestion was accelerated by using elevated temperature with ultrasonication. The whole time of cell treatment was 30 min. After that, single-cell digest peptides were transferred into an LC column directly through a true zero dead volume union, to minimize protein transfer loss. A homemade 22 μm i.d. nano-LC packing column with 3 μm i.d. ESI tip was used in the device to achieve ultrasensitive detection. A 30 min elution program was applied to analysis of the single-cell proteome. Therefore, the total time needed for a single-cell analysis was only 1 h. In an analysis of 10 single HeLa cells, a maximum of 328 proteins were identified in one cell by using an Orbitrap Fusion Tribrid MS instrument, and the detection limit was estimated at around 1.7-170 zmol. Such a sensitivity of the iPAD-1 was ∼120-fold higher than that of our previously developed iPAD-100 system. (1) Prominent cellular heterogeneity in protein expressive profiling was observed. Furthermore, we roughly estimated the phases of the cell cycle of tested HeLa cells by the amount of core histone proteins.
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Affiliation(s)
- Xi Shao
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Xuantang Wang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Sheng Guan
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Haizhu Lin
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
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Choi SB, Lombard-Banek C, Muñoz-LLancao P, Manzini MC, Nemes P. Enhanced Peptide Detection Toward Single-Neuron Proteomics by Reversed-Phase Fractionation Capillary Electrophoresis Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:913-922. [PMID: 29147852 DOI: 10.1007/s13361-017-1838-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/12/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
The ability to detect peptides and proteins in single cells is vital for understanding cell heterogeneity in the nervous system. Capillary electrophoresis (CE) nanoelectrospray ionization (nanoESI) provides high-resolution mass spectrometry (HRMS) with trace-level sensitivity, but compressed separation during CE challenges protein identification by tandem HRMS with limited MS/MS duty cycle. Here, we supplemented ultrasensitive CE-nanoESI-HRMS with reversed-phase (RP) fractionation to enhance identifications from protein digest amounts that approximate to a few mammalian neurons. An ~1 to 20 μg neuronal protein digest was fractionated on a RP column (ZipTip), and 1 ng to 500 pg of peptides were analyzed by a custom-built CE-HRMS system. Compared with the control (no fractionation), RP fractionation improved CE separation (theoretical plates ~274,000 versus 412,000 maximum, resp.), which enhanced detection sensitivity (2.5-fold higher signal-to-noise ratio), minimized co-isolation spectral interferences during MS/MS, and increased the temporal rate of peptide identification by up to ~57%. From 1 ng of protein digest (<5 neurons), CE with RP fractionation identified 737 protein groups (1,753 peptides), or ~480 protein groups (~1,650 peptides) on average per analysis. The approach was scalable to 500 pg of protein digest (~a single neuron), identifying 225 protein groups (623 peptides) in technical triplicates, or 141 protein groups on average per analysis. Among identified proteins, 101 proteins were products of genes that are known to be transcriptionally active in single neurons during early development of the brain, including those involved in synaptic transmission and plasticity and cytoskeletal organization. Graphical abstract ᅟ.
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Affiliation(s)
- Sam B Choi
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Camille Lombard-Banek
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Pablo Muñoz-LLancao
- Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University, Washington, DC, 20052, USA
| | - M Chiara Manzini
- Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University, Washington, DC, 20052, USA
| | - Peter Nemes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
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Zhang L, Jia X, Jin JO, Lu H, Tan Z. Recent 5-year Findings and Technological Advances in the Proteomic Study of HIV-associated Disorders. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:110-120. [PMID: 28391008 PMCID: PMC5415375 DOI: 10.1016/j.gpb.2016.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/03/2016] [Accepted: 11/24/2016] [Indexed: 12/24/2022]
Abstract
Human immunodeficiency virus-1 (HIV-1) mainly relies on host factors to complete its life cycle. Hence, it is very important to identify HIV-regulated host proteins. Proteomics is an excellent technique for this purpose because of its high throughput and sensitivity. In this review, we summarized current technological advances in proteomics, including general isobaric tags for relative and absolute quantitation (iTRAQ) and stable isotope labeling by amino acids in cell culture (SILAC), as well as subcellular proteomics and investigation of posttranslational modifications. Furthermore, we reviewed the applications of proteomics in the discovery of HIV-related diseases and HIV infection mechanisms. Proteins identified by proteomic studies might offer new avenues for the diagnosis and treatment of HIV infection and the related diseases.
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Affiliation(s)
- Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
| | - Xiaofang Jia
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jun-O Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Hongzhou Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhimi Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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Choi SB, Zamarbide M, Manzini MC, Nemes P. Tapered-Tip Capillary Electrophoresis Nano-Electrospray Ionization Mass Spectrometry for Ultrasensitive Proteomics: the Mouse Cortex. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:597-607. [PMID: 27853976 DOI: 10.1007/s13361-016-1532-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
Ultrasensitive characterization of the proteome raises the potential to understand how differential gene expression orchestrates cell heterogeneity in the brain. Here, we report a microanalytical capillary electrophoresis nano-flow electrospray ionization (CE-nanoESI) interface for mass spectrometry to enable the measurement of limited amounts of proteins in the mouse cortex. Our design integrates a custom-built CE system to a tapered-tip metal emitter in a co-axial sheath-flow configuration. This interface can be constructed in <15 min using readily available components, facilitating broad adaptation. Tapered-tip CE-nanoESI generates stable electrospray by reproducibly anchoring the Taylor cone, minimizes sample dilution in the ion source, and ensures efficient ion generation by sustaining the cone-jet spraying regime. Parallel reaction monitoring provided a 260-zmol lower limit of detection for angiotensin II (156,000 copies). CE was able to resolve a complex mixture of peptides in ~330,000 theoretical plates and identify ~15 amol (~1 pg) of BSA or cytochrome c. Over 30 min of separation, 1 ng protein digest from the mouse cortex yielded 217 nonredundant proteins encompassing a ~3-log-order concentration range using a quadrupole time-of-flight mass spectrometer. Identified proteins included many products from genes that are traditionally used to mark oligodendrocytes, astrocytes, and microglia. Finally, key proteins involved in neurodegenerative disorders were detected (e.g., parkinsonism and spastic paraplegia). CE-nanoESI-HRMS delivers sufficient sensitivity to detect proteins in limited amounts of tissues and cell populations to help understand how gene expression differences maintain cell heterogeneity in the brain. Graphical Abstract ᅟ.
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Affiliation(s)
- Sam B Choi
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Marta Zamarbide
- Department of Pharmacology and Physiology, The George Washington University, Washington, DC, 20037, USA
| | - M Chiara Manzini
- Department of Pharmacology and Physiology, The George Washington University, Washington, DC, 20037, USA
| | - Peter Nemes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
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Liu Y, Yan G, Gao M, Deng C, Zhang X. Integrated system for extraction, purification, and digestion of membrane proteins. Anal Bioanal Chem 2016; 408:3495-502. [PMID: 26922343 DOI: 10.1007/s00216-016-9427-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/26/2016] [Accepted: 02/16/2016] [Indexed: 11/29/2022]
Abstract
An integrated system was developed for directly processing living cells into peptides of membrane proteins. Living cells were directly injected into the system and cracked in a capillary column by ultrasonic treatment. Owing to hydrophilicity for broken pieces of the cell membrane, the obtained membranes were retained in a well-designed bi-filter. While cytoplasm proteins were eluted from the bi-filter, the membranes were dissolved and protein released by flushing 4% SDS buffer through the bi-filter. The membrane proteins were subsequently transferred into a micro-reactor and covalently bound in the reactor for purification and digestion. As the system greatly simplified the whole pretreatment processes and minimized both sample loss and contamination, it could be used to analyze the membrane proteome samples of thousand-cell-scales with acceptable reliability and stability. We totally identified 1348 proteins from 5000 HepG2 cells, 615 of which were annotated as membrane proteins. In contrast, with conventional method, only 233 membrane proteins were identified. It is adequately demonstrated that the integrated system shows promising practicability for the membrane proteome analysis of small amount of cells.
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Affiliation(s)
- Yiying Liu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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Lombard-Banek C, Moody SA, Nemes P. Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus) Embryo. Angew Chem Int Ed Engl 2016; 55:2454-8. [PMID: 26756663 PMCID: PMC4755155 DOI: 10.1002/anie.201510411] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/21/2015] [Indexed: 01/05/2023]
Abstract
We advance mass spectrometry from a cell population‐averaging tool to one capable of quantifying the expression of diverse proteins in single embryonic cells. Our instrument combines capillary electrophoresis (CE), electrospray ionization, and a tribrid ultrahigh‐resolution mass spectrometer (HRMS) to enable untargeted (discovery) proteomics with ca. 25 amol lower limit of detection. CE‐μESI‐HRMS enabled the identification of 500–800 nonredundant protein groups by measuring 20 ng, or <0.2% of the total protein content in single blastomeres that were isolated from the 16‐cell frog (Xenopus laevis) embryo, amounting to a total of 1709 protein groups identified between n=3 biological replicates. By quantifying ≈150 nonredundant protein groups between all blastomeres and replicate measurements, we found significant translational cell heterogeneity along multiple axes of the embryo at this very early stage of development when the transcriptional program of the embryo has yet to begin.
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Affiliation(s)
- Camille Lombard-Banek
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, 800 22ndStreet, NW, Suite 4000, Washington, DC, 20052, USA
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC, 20052, USA
| | - Peter Nemes
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, 800 22ndStreet, NW, Suite 4000, Washington, DC, 20052, USA.
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Lombard‐Banek C, Moody SA, Nemes P. Single‐Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16‐Cell Frog (
Xenopus
) Embryo. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510411] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Camille Lombard‐Banek
- Department of Chemistry W. M. Keck Institute for Proteomics Technology and Applications The George Washington University 800 22ndStreet, NW, Suite 4000 Washington DC 20052 USA
| | - Sally A. Moody
- Department of Anatomy and Regenerative Biology The George Washington University Washington DC 20052 USA
| | - Peter Nemes
- Department of Chemistry W. M. Keck Institute for Proteomics Technology and Applications The George Washington University 800 22ndStreet, NW, Suite 4000 Washington DC 20052 USA
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Chen Q, Yan G, Zhang X. Applying multiple proteases to direct digestion of hundred-scale cell samples for proteome analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1389-1394. [PMID: 26147478 DOI: 10.1002/rcm.7230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/16/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Analyzing the proteome on the scale of only several hundred cells with mass spectrometry has great significance for applications with limited sample amounts. We applied multiple proteases to the direct digestion of cells and compared the identified proteins both qualitatively and quantitatively. METHODS Three hundred cells were directly digested by trypsin, chymotrypsin, or the combination of trypsin and chymotrypsin. The peptides were identified using a LTQ-Orbitrap XL, and data were analyzed using MaxQuant software. RESULTS Different proteases produced different identified protein numbers. Trypsin proved to be the best choice for generating the largest protein number, while other proteases complemented the identification results of trypsin by increasing protein sequence coverage. Concerning the quantitative perspective, using trypsin would produce the biggest number of proteins quantifiable by intensity-based absolute quantification (iBAQ). CONCLUSIONS When hundred-scale cell samples are analyzed, an optimum choice of proteases should be made to realize different analytical objectives.
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Affiliation(s)
- Qi Chen
- Department of Chemistry, Fudan University, No. 220 Handan Rd., Shanghai, 200433, China
| | - Guoquan Yan
- Department of Chemistry, Fudan University, No. 220 Handan Rd., Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry, Fudan University, No. 220 Handan Rd., Shanghai, 200433, China
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Chen Q, Yan G, Gao M, Zhang X. Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis. Anal Chem 2015; 87:6674-80. [PMID: 26061007 DOI: 10.1021/acs.analchem.5b00808] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Single-cell proteome analysis has always been an exciting goal because it provides crucial information about cellular heterogeneity and dynamic change. Here we presented an integrated proteome analysis device (iPAD) for 100 living cells (iPAD-100) that might be suitable for single-cell analysis. Once cells were cultured, the iPAD-100 could be applied to inject 100 living cells, to transform the living cells into peptides, and to produce protein identification results with total automation. Due to the major obstacle for detection limit of mass spectrometry, we applied the iPAD-100 to analyze the proteome of 100 cells. In total, 813 proteins were identified in a DLD-cell proteome by three duplicate runs. Gene Ontology analysis revealed that proteins from different cellular compartments were well-represented, including membrane proteins. The iPAD-100 greatly simplified the sampling process, reduced sample loss, and prevented contamination. As a result, proteins whose copy numbers were lower than 1000 were identified from 100-cell samples with the iPAD-100, showing that a detection limit of 200 zmol was achieved. With increased sensitivity of mass spectrometry, the iPAD-100 may be able to reveal bountiful proteome information from a single cell in the near future.
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Affiliation(s)
- Qi Chen
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Guoquan Yan
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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