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Huang Y, Shao X, Liu Y, Yan K, Ying W, He F, Wang D. RUPE-phospho: Rapid Ultrasound-Assisted Peptide-Identification-Enhanced Phosphoproteomics Workflow for Microscale Samples. Anal Chem 2023; 95:17974-17980. [PMID: 38011496 DOI: 10.1021/acs.analchem.3c02623] [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: 11/29/2023]
Abstract
Global phosphoproteome profiling can provide insights into cellular signaling and disease pathogenesis. To achieve comprehensive phosphoproteomic analyses with minute quantities of material, we developed a rapid and sensitive phosphoproteomics sample preparation strategy based on ultrasound. We found that ultrasonication-assisted digestion can significantly improve peptide identification by 20% due to the generation of longer peptides that can be detected by mass spectrometry. By integrating this rapid ultrasound-assisted peptide-identification-enhanced proteomic method (RUPE) with streamlined phosphopeptide enrichment steps, we established RUPE-phospho, a fast and efficient strategy to characterize protein phosphorylation in mass-limited samples. This approach dramatically reduces the sample loss and processing time: 24 samples can be processed in 3 h; 5325 phosphosites, 4549 phosphopeptides, and 1888 phosphoproteins were quantified from 5 μg of human embryonic kidney (HEK) 293T cell lysate. In addition, 9219 phosphosites were quantified from 1-2 mg of OCT-embedded mouse brain with 120 min streamlined RUPE-phospho workflow. RUPE-phospho facilitates phosphoproteome profiling for microscale samples and will provide a powerful tool for proteomics-driven precision medicine research.
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Affiliation(s)
- Yuanxuan Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xianfeng Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuanyuan Liu
- The π-HuB Project Infrastructure, Guangzhou 510000, China
| | - Kehan Yan
- The π-HuB Project Infrastructure, Guangzhou 510000, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- The π-HuB Project Infrastructure, Guangzhou 510000, China
- Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Dongxue Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Science-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- The π-HuB Project Infrastructure, Guangzhou 510000, China
- Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
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2
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Rodzik A, Railean V, Pomastowski P, Buszewski B, Szumski M. Immobilized enzyme microreactors for analysis of tryptic peptides in β-casein and β-lactoglobulin. Sci Rep 2023; 13:16551. [PMID: 37783762 PMCID: PMC10545664 DOI: 10.1038/s41598-023-43521-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: 07/26/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
In this study, our primary objective was to develop an effective analytical method for studying trypsin-digested peptides of two proteins commonly found in cow's milk: β-casein (βCN) and β-lactoglobulin (βLG). To achieve this, we employed two distinct approaches: traditional in-gel protein digestion and protein digestion using immobilized enzyme microreactors (μ-IMER). Both methods utilized ZipTip pipette tips filled with C18 reverse phase media for sample concentration. The μ-IMER was fabricated through a multi-step process that included preconditioning the capillary, modifying its surface, synthesizing a monolithic support, and further surface modification. Its performance was evaluated under HPLC chromatography conditions using a small-molecule trypsin substrate (BAEE). Hydrolysates from both digestion methods were analyzed using MALDI-TOF MS. Our findings indicate that the μ-IMER method demonstrated superior sequence coverage for oxidized molecules in βCN (33 ± 1.5%) and βLG (65 ± 3%) compared to classical in-gel digestion (20 ± 2% for βCN; 49 ± 2% for βLG). The use of ZipTips further improved sequence coverage in both classical in-gel digestion (26 ± 1% for βCN; 60 ± 4% for βLG) and μ-IMER (41 ± 3% for βCN; 80 ± 5% for βLG). Additionally, phosphorylations were identified. For βCN, no phosphorylation was detected using classical digestion, but the use of ZipTips showed a value of 27 ± 4%. With μ-IMER and μ-IMER-ZipTip, the values increased to 30 ± 2% and 33 ± 1%, respectively. For βLG, the use of ZipTip enabled the detection of a higher percentage of modified peptides in both classical (79 ± 2%) and μ-IMER (79 ± 4%) digestions. By providing a comprehensive comparison of traditional in-gel digestion and μ-IMER methods, this study offers valuable insights into the advantages and limitations of each approach, particularly in the context of complex biological samples. The findings set a new benchmark in protein digestion and analysis, highlighting the potential of μ-IMER systems for enhanced sequence coverage and post-translational modification detection.
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Affiliation(s)
- Agnieszka Rodzik
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland.
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland.
| | - Viorica Railean
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland
| | - Michał Szumski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland.
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Tian Y, Lai J, Li C, Sun J, Liu K, Zhao C, Zhang M. Poly( N-acryloyl glycinamide- co- N-acryloxysuccinimide) Nanoparticles: Tunable Thermo-Responsiveness and Improved Bio-Interfacial Adhesion for Cell Function Regulation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:7867-7877. [PMID: 36740782 DOI: 10.1021/acsami.2c22267] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Poly(N-acryloyl glycinamide) (PNAGA) can form high-strength hydrogen bonds (H-bonds) through the dual amide motifs in the side chain, allowing the polymer to exhibit gelation behavior and an upper critical solution temperature (UCST) property. These features make PNAGA a candidate platform for biomedical devices. However, most applications focused on PNAGA hydrogels, while few focused on PNAGA nanoparticles. Improving the UCST tunability and bio-interfacial adhesion of the PNAGA nanoparticles may expand their applications in biomedical fields. To address the issues, we established a reactive H-bond-type P(NAGA-co-NAS) copolymer via reversible addition-fragmentation chain transfer polymerization of NAGA and N-acryloxysuccinimide (NAS) monomers. The UCST behaviors and the bio-interfacial adhesion toward the proteins and cells along with the potential application of the copolymer nanoparticles were investigated in detail. Taking advantage of the enhanced H-bonding and reactivity, the copolymer exhibited a tunable UCST in a broad temperature range, showing thermo-reversible transition between nanoparticles (PNPs) and soluble chains; the PNPs efficiently bonded proteins into nano-biohybrids while keeping the secondary structure of the protein, and more importantly, they also exhibited good adhesion ability to the cell membrane and significantly inhibited cell-specific propagation. These features suggest broad prospects for the P(NAGA-co-NAS) nanoparticles in the fields of biosensors, protein delivery, cell surface decoration, and cell-specific function regulation.
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Affiliation(s)
- Yueyi Tian
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin300192, China
| | - Jiahui Lai
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin300192, China
| | - Chen Li
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin300192, China
| | - Jialin Sun
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin300192, China
| | - Kang Liu
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, China
| | - Chuanzhuang Zhao
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, China
| | - Mingming Zhang
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin300192, China
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Gil J, Krimm I, Dugas V, Demesmay C. Preparation of miniaturized hydrophilic affinity monoliths: Towards a reduction of non-specific interactions and an increased target protein density. J Chromatogr A 2023; 1687:463670. [PMID: 36463648 DOI: 10.1016/j.chroma.2022.463670] [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: 10/17/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022]
Abstract
In affinity chromatography, non-specific interactions between the ligands and the affinity column may affect the results, leading to misinterpretations during the investigation of protein-ligand interactions (detection of false positives in ligand screening, lack of specificity in purification). Such non-specific interactions may arise both from the underlying support or from the target protein itself. If the second ones are protein-dependent (and cannot be studied in a general framework), the first ones occur in the same way regardless of the immobilized target. We propose a methodology to identify the origin of such non-specific interactions with the underlying material of the affinity column. This methodology relies on the systematic investigation of the retention behavior of a set of 41 low-molecular weight compounds covering a wide chemical space (net charge, log D, functionality). We first demonstrate that the main source of non-specific interactions on the most commonly used GMA-co-EDMA monolith comes from hydrophobic effects. To reduce such non-specific interactions, we developed a new hydrophilic glycidyl methacrylate-based monolith by replacing the EDMA crosslinker by the more hydrophilic NN' Methylenebisacrylamide (MBA). Optimization of the synthesis parameters (monomer content, initiation type, temperature) has focused on the reduction of non-specific interaction with the monolithic support while maximizing the amount of protein that can be grafted onto the monolith at the issue of its synthesis. The retention data of the 41 test solutes on the new poly(GMA-co-MBA) monolith shows a drastic reduction of non-specific interactions except for cationic compounds. The particular behavior of cationic compounds is due to their electrostatic interactions with carboxylic groups resulting from the partial acidic hydrolysis of amide groups of MBA during the epoxide ring opening step. So, the ring opening step in acidic media was replaced by a hot water treatment to avoid side reaction on MBA. The new monolith poly(GMA-co-MBA) not only has improved hydrophilic surface properties but also a higher protein density (16 ± 0.8 pmol cm-1 instead of 8 ± 0.3 pmol cm-1). To highlight the benefits of this new hydrophilic monolith for affinity chromatographic studies, frontal affinity chromatography experiments were conducted on these monoliths grafted with con A.
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Affiliation(s)
- Julie Gil
- Institut des Sciences Analytiques, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Isabelle Krimm
- Centre Léon Bérard, INSERM 1052, CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Small Molecules for Biological Targets Team, Université de Lyon, Université Claude Bernard Lyon 1, Lyon 69373, France
| | - Vincent Dugas
- Institut des Sciences Analytiques, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France.
| | - Claire Demesmay
- Institut des Sciences Analytiques, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
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Liu G, Du Y, Fu T, Han Y, Pan L, Kang J. Profiling protein interactions by purification with capillary monolithic affinity column in combination with label-free quantitative proteomics. J Chromatogr A 2022; 1676:463273. [PMID: 35767907 DOI: 10.1016/j.chroma.2022.463273] [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: 01/16/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 10/17/2022]
Abstract
An approach for profiling protein-protein interactions by using affinity purification with capillary monolithic immobilized metal affinity chromatography column (cm-IMAC) in combination with label free quantitative proteomics was described in the present work. The cm-IMAC columns were prepared in a single step by copolymerization of the function monomer, namely (S)-2,2'-((1-carboxy-5-(pent‑4-enamido)pentyl)azanediyl)diacetic acid which provide a nitrilotriacetate (NTA) moiety to form chelated complexation with Ni (II) ions, inside the fused silica capillaries. The His6-tagged bait protein can be easily immobilized on the cm-IMAC columns through the formation of chelating complexation with the NTA-Ni (II) functional groups of the matrix. The cm-IMAC columns were used to explore protein-protein interactions (PPIs) on a proteomic scale when combined with label-free proteomics. A known interaction pair of proteins, namely NDP52 (amino acid sequence 10-126) and NAP1 (33-75) as well as Bcl-2 family proteins were used for proof of concept. New interactors of Bcl-XL were identified and validated by co-immunoprecipitation.
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Affiliation(s)
- Guizhen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of physical science and technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of physical science and technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tao Fu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Ying Han
- School of life science and technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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Rainer T, Egger AS, Zeindl R, Tollinger M, Kwiatkowski M, Müller T. 3D-Printed High-Pressure-Resistant Immobilized Enzyme Microreactor (μIMER) for Protein Analysis. Anal Chem 2022; 94:8580-8587. [PMID: 35678765 PMCID: PMC9218953 DOI: 10.1021/acs.analchem.1c05232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Additive manufacturing
(3D printing) has greatly revolutionized
the way researchers approach certain technical challenges. Despite
its outstanding print quality and resolution, stereolithography (SLA)
printing is cost-effective and relatively accessible. However, applications
involving mass spectrometry (MS) are few due to residual oligomers
and additives leaching from SLA-printed devices that interfere with
MS analyses. We identified the crosslinking agent urethane dimethacrylate
as the main contaminant derived from SLA prints. A stringent washing
and post-curing protocol mitigated sample contamination and rendered
SLA prints suitable for MS hyphenation. Thereafter, SLA printing was
used to produce 360 μm I.D. microcolumn chips with excellent
structural properties. By packing the column with polystyrene microspheres
and covalently immobilizing pepsin, an exceptionally effective microscale
immobilized enzyme reactor (μIMER) was created. Implemented
in an online liquid chromatography-MS/MS setup, the protease microcolumn
enabled reproducible protein digestion and peptide mapping with 100%
sequence coverage obtained for three different recombinant proteins.
Additionally, when assessing the μIMER digestion efficiency
for complex proteome samples, it delivered a 144-fold faster and significantly
more efficient protein digestion compared to 24 h for bulk digestion.
The 3D-printed μIMER withstands remarkably high pressures above
130 bar and retains its activity for several weeks. This versatile
platform will enable researchers to produce tailored polymer-based
enzyme reactors for various applications in analytical chemistry and
beyond.
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Affiliation(s)
- Tobias Rainer
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Anna-Sophia Egger
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Ricarda Zeindl
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Thomas Müller
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
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Su Y, Wang X, Yang Y, Yang L, Xu R, Tian R. Zwitter-ionic monolith-based spintip column coupled with Evosep One liquid chromatography for high-throughput proteomic analysis. J Chromatogr A 2022; 1675:463122. [PMID: 35623190 DOI: 10.1016/j.chroma.2022.463122] [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: 02/21/2022] [Revised: 04/25/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022]
Abstract
A high-throughput proteomic workflow with good sensitivity and reproducibility is highly demanding for proteomic studies of large clinical cohorts. We present a workflow that seamlessly integrates the zwitter-ionic monolith-based spintip (ZIM-Tip) with the Evosep One liquid chromatography system to address this challenge. Disposable ZIM-Tips were prepared with satisfying permeability based on photo-initiated free radical polymerization. Sample preparation steps, including ion-exchange-based protein concentration, reduction, alkylation, and enzymatic digestion, were processed on the ZIM-Tips in 2 h with about 10% sample loss. The peptides recovered from ZIM-Tips were directly loaded on Evotips for desalting and proteomic data acquisition. In one-hour high performance liquid chromatography-MS/MS run, more than 4000 proteins were consistently identified from 1 µg of cell lysate using timsTOF Pro-mass spectrometer in data-dependent acquisition mode (DDA). At least 20 samples with protein amount of 1 µg could be processed each day. Good intra- and inter-day precision in quantification were demonstrated with median coefficient of variation (CV) values of less than 20% and 30%, respectively. The average Pearson correlation coefficients of each two sets of samples are 0.934 and 0.901, respectively. Collectively, the ZIM-Tip technology offers an useful solution for clinical cohort studies with demand for large sample amounts and low sample input while maintaining in-depth proteome coverage.
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Affiliation(s)
- Yiran Su
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Wang
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China; Shenzhen People's Hospital, The First Clinical Medical College of Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lijun Yang
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China; Shenzhen People's Hospital, The First Clinical Medical College of Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruilian Xu
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China; Shenzhen People's Hospital, The First Clinical Medical College of Southern University of Science and Technology, Shenzhen 518055, China.
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China; Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
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Evaluation of Fast and Sensitive Proteome Profiling of FF and FFPE Kidney Patient Tissues. Molecules 2022; 27:molecules27031137. [PMID: 35164409 PMCID: PMC8838561 DOI: 10.3390/molecules27031137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
The application of proteomics to fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) human tissues is an important development spurred on by requests from stakeholder groups in clinical fields. One objective is to complement current diagnostic methods with new specific molecular information. An important goal is to achieve adequate and consistent protein recovery across and within large-scale studies. Here, we describe development of several protocols incorporating mass spectrometry compatible detergents, including Rapigest, PPS, and ProteaseMax. Methods were applied on 4 and 15 μm thick FF tissues, and 4 μm thick FFPE tissues. We evaluated sensitivity and repeatability of the methods and found that the protocol containing Rapigest enabled detection of 630 proteins from FF tissue of 1 mm2 and 15 μm thick, whereas 498 and 297 proteins were detected with the protocols containing ProteaseMax and PPS, respectively. Surprisingly, PPS-containing buffer showed good extraction of the proteins from 4 μm thick FFPE tissue with the average of 270 protein identifications (1 mm2), similar to the results on 4 μm thick FF. Moreover, we found that temperature increases during incubation with urea on 4 μm thick FF tissue revealed a decrease in the number of identified proteins and increase in the number of the carbamylated peptides.
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Sun J, Lu J, Li C, Tian Y, Liu K, Liu L, Zhao C, Zhang M. Design of a UCST Polymer with Strong Hydrogen Bonds and Reactive Moieties for Facile Polymer-Protein Hybridization. Biomacromolecules 2022; 23:1291-1301. [PMID: 35049291 DOI: 10.1021/acs.biomac.1c01520] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polymer-protein hybrids have been extensively used in biomedical fields. Polymers with upper critical solution temperature (UCST) behaviors can form a hydrated coacervate phase below the cloud point (Tcp), providing themselves the opportunity to directly capture hydrophilic proteins and form hybrids in aqueous solutions. However, it is always a challenge to obtain a UCST polymer that could aggregate at a high temperature at a relatively low concentration and also efficiently bind with proteins. In this work, a UCST polymer reactive with proteins was designed, and its temperature responsiveness and protein-capture ability were investigated in detail. The polymer was synthesized by the reversible addition-fragmentation chain transfer (RAFT) polymerization of acrylamide (AAm) and N-acryloxysuccinimide (NAS). Interestingly, taking advantage of the partial hydrolysis of NAS into acrylic acid (AAc), the obtained P(AAm-co-NAS-co-AAc) polymer exhibited an excellent UCST behavior and possessed good protein-capture ability. It showed a relatively higher Tcp (81 °C) at a lower concentration (0.1 wt %) and quickly formed polymer-protein hybrids with high protein loading and without losing protein bioactivity, and both the polymer and polymer-protein nanoparticles showed good cytocompatibility. All the findings are attributed to the unique structure of the polymer, which provided not only the strong and stable hydrogen bonds but also the quick and mild reactivity. The work offers an easy and mild strategy for polymer-protein hybridization directly in aqueous solutions, which may find applications in biomedical fields.
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Affiliation(s)
- Jialin Sun
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
| | - Jianlei Lu
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Chen Li
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
| | - Yueyi Tian
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
| | - Kang Liu
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Lingrong Liu
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
| | - Chuanzhuang Zhao
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Mingming Zhang
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
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10
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Wouters B, Currivan S, Abdulhussain N, Hankemeier T, Schoenmakers P. Immobilized-enzyme reactors integrated into analytical platforms: Recent advances and challenges. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Poddar S, Sharmeen S, Hage DS. Affinity monolith chromatography: A review of general principles and recent developments. Electrophoresis 2021; 42:2577-2598. [PMID: 34293192 DOI: 10.1002/elps.202100163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/07/2021] [Accepted: 07/18/2021] [Indexed: 12/28/2022]
Abstract
Affinity monolith chromatography (AMC) is a liquid chromatographic technique that utilizes a monolithic support with a biological ligand or related binding agent to isolate, enrich, or detect a target analyte in a complex matrix. The target-specific interaction exhibited by the binding agents makes AMC attractive for the separation or detection of a wide range of compounds. This article will review the basic principles of AMC and recent developments in this field. The supports used in AMC will be discussed, including organic, inorganic, hybrid, carbohydrate, and cryogel monoliths. Schemes for attaching binding agents to these monoliths will be examined as well, such as covalent immobilization, biospecific adsorption, entrapment, molecular imprinting, and coordination methods. An overview will then be given of binding agents that have recently been used in AMC, along with their applications. These applications will include bioaffinity chromatography, immunoaffinity chromatography, immobilized metal-ion affinity chromatography, and dye-ligand or biomimetic affinity chromatography. The use of AMC in chiral separations and biointeraction studies will also be discussed.
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Affiliation(s)
- Saumen Poddar
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
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12
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Hakala T, Bialas F, Toprakcioglu Z, Bräuer B, Baumann KN, Levin A, Bernardes GJL, Becker CFW, Knowles TPJ. Continuous Flow Reactors from Microfluidic Compartmentalization of Enzymes within Inorganic Microparticles. ACS APPLIED MATERIALS & INTERFACES 2020; 12:32951-32960. [PMID: 32589387 PMCID: PMC7383928 DOI: 10.1021/acsami.0c09226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Compartmentalization and selective transport of molecular species are key aspects of chemical transformations inside the cell. In an artificial setting, the immobilization of a wide range of enzymes onto surfaces is commonly used for controlling their functionality but such approaches can restrict their efficacy and expose them to degrading environmental conditions, thus reducing their activity. Here, we employ an approach based on droplet microfluidics to generate enzyme-containing microparticles that feature an inorganic silica shell that forms a semipermeable barrier. We show that this porous shell permits selective diffusion of the substrate and product while protecting the enzymes from degradation by proteinases and maintaining their functionality over multiple reaction cycles. We illustrate the power of this approach by synthesizing microparticles that can be employed to detect glucose levels through simultaneous encapsulation of two distinct enzymes that form a controlled reaction cascade. These results demonstrate a robust, accessible, and modular approach for the formation of microparticles containing active but protected enzymes for molecular sensing applications and potential novel diagnostic platforms.
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Affiliation(s)
- Tuuli
A. Hakala
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Friedrich Bialas
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Street 38, 1090 Vienna, Austria
| | - Zenon Toprakcioglu
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Birgit Bräuer
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Street 38, 1090 Vienna, Austria
| | - Kevin N. Baumann
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Aviad Levin
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Gonçalo J. L. Bernardes
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Instituto
de Medicina Molecular, Faculdade de Medicina
de Universidad de Lisboa, 1649-028 Lisboa, Portugal
| | - Christian F. W. Becker
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Street 38, 1090 Vienna, Austria
| | - Tuomas P. J. Knowles
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Cavendish
Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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13
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Simplification of affinity macroporous monolith microfluidic column synthesis and its ability for protein separation. J Pharm Biomed Anal 2020; 181:113099. [DOI: 10.1016/j.jpba.2020.113099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 01/10/2023]
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14
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Recent advances in preparation and applications of monolithic chiral stationary phases. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115774] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Current trends in affinity-based monoliths in microextraction approaches: A review. Anal Chim Acta 2019; 1084:1-20. [DOI: 10.1016/j.aca.2019.07.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/15/2022]
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16
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Recent advances in the fabrication and application of nanomaterial-based enzymatic microsystems in chemical and biological sciences. Anal Chim Acta 2019; 1067:31-47. [DOI: 10.1016/j.aca.2019.02.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 02/09/2019] [Accepted: 02/12/2019] [Indexed: 11/24/2022]
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17
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Lin H, Zhang C, Lin Y, Chang Y, Crommen J, Wang Q, Jiang Z, Guo J. A strategy for screening trypsin inhibitors from traditional Chinese medicine based on a monolithic capillary immobilized enzyme reactor coupled with offline liquid chromatography and mass spectrometry. J Sep Sci 2019; 42:1980-1989. [DOI: 10.1002/jssc.201900169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Hang Lin
- Institute of Pharmaceutical AnalysisCollege of PharmacyJinan University Guangzhou P. R. China
| | - Changfa Zhang
- School of Stomatology and MedicineFoshan University Foshan P. R. China
| | - Yuanjing Lin
- Institute of Pharmaceutical AnalysisCollege of PharmacyJinan University Guangzhou P. R. China
| | - Yiqun Chang
- Faculty of Medicine and HealthUniversity of Sydney Sydney NSW Australia
| | - Jacques Crommen
- Institute of Pharmaceutical AnalysisCollege of PharmacyJinan University Guangzhou P. R. China
- Laboratory of Analytical Pharmaceutical ChemistryDepartment of Pharmaceutical SciencesUniversity of Liege Liege Belgium
| | - Qiqin Wang
- Institute of Pharmaceutical AnalysisCollege of PharmacyJinan University Guangzhou P. R. China
| | - Zhengjin Jiang
- Institute of Pharmaceutical AnalysisCollege of PharmacyJinan University Guangzhou P. R. China
- Department of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug ResearchJinan University Guangzhou P. R. China
| | - Jialiang Guo
- Institute of Pharmaceutical AnalysisCollege of PharmacyJinan University Guangzhou P. R. China
- School of Stomatology and MedicineFoshan University Foshan P. R. China
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18
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Rapid proteolytic digestion and peptide separation using monolithic enzyme microreactor coupled with capillary electrophoresis. J Pharm Biomed Anal 2019; 165:129-134. [DOI: 10.1016/j.jpba.2018.11.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 11/21/2022]
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19
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Naldi M, Tramarin A, Bartolini M. Immobilized enzyme-based analytical tools in the -omics era: Recent advances. J Pharm Biomed Anal 2018; 160:222-237. [DOI: 10.1016/j.jpba.2018.07.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023]
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20
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Lynch KB, Ren J, Beckner MA, He C, Liu S. Monolith columns for liquid chromatographic separations of intact proteins: A review of recent advances and applications. Anal Chim Acta 2018; 1046:48-68. [PMID: 30482303 DOI: 10.1016/j.aca.2018.09.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 01/20/2023]
Abstract
In this article we survey 256 references (with an emphasis on the papers published in the past decade) on monolithic columns for intact protein separation. Protein enrichment and purification are included in the broadly defined separation. After a brief introduction, we describe the types of monolithic columns and modes of chromatographic separations employed for protein separations. While the majority of the work is still in the research and development phase, papers have been published toward utilizing monolithic columns for practical applications. We survey these papers as well in this review. Characteristics of selected methods along with their pros and cons will also be discussed.
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Affiliation(s)
- Kyle B Lynch
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Jiangtao Ren
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Matthew A Beckner
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Chiyang He
- School of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Textile Road, Wuhan, 430073, PR China
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States.
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21
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Wang L, Zhao Y, Zhang Y, Zhang T, Kool J, Somsen GW, Wang Q, Jiang Z. Online screening of acetylcholinesterase inhibitors in natural products using monolith-based immobilized capillary enzyme reactors combined with liquid chromatography-mass spectrometry. J Chromatogr A 2018; 1563:135-143. [DOI: 10.1016/j.chroma.2018.05.069] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/26/2018] [Accepted: 05/29/2018] [Indexed: 12/18/2022]
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22
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Xiong Y, Zhang Y, Yao J, Yan G, Lu H. A Streamlined Sample Preparation Method for Mass Spectrometric Analysis. ACTA ACUST UNITED AC 2018; 78:5.8.1-5.8.8. [PMID: 30040186 DOI: 10.1002/cpcb.40] [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: 11/10/2022]
Abstract
Mass spectrometry-based proteomic technology experienced remarkable advancement in the past decades. However, their application was still hampered by the complexity of sample preparation. Conventional strategies for sample preparation incorporate multiple time-consuming steps, including cell lysis, protein extraction, protease cleavage, and desalting. Thus, we explored a simplified method (the cell-absorb method) during which living cells were absorbed into vacuum-dried polyacrylamide gel and directly digested in gel into peptides for subsequent LC-MS/MS analysis. As a consequence, both of the steps for cell lysis and protein extraction involved in traditional protocol were skipped. In addition to the decrease in time, more proteins were identified. Indeed, 3022 proteins were identified by the cell-absorb method. Meanwhile, only 2642 and 2420 proteins were identified by the classical SDS-PAGE based method and the reported gel absorption-based method, respectively. The cell-absorb method exhibited apparent advantage in terms of the depth of proteome coverage. Furthermore, the number of proteins identified show excellent reproducibility with a CV (coefficient of variation) of 0.03 among three replicates using the cell-absorb method. These advantages suggest that cell-absorb method is a promising choice for mapping the whole proteome of cells. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yun Xiong
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Ying Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jun Yao
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guoquan Yan
- Department of Chemistry, Fudan University, Shanghai, China
| | - Haojie Lu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
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23
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Martinović T, Šrajer Gajdošik M, Josić D. Sample preparation in foodomic analyses. Electrophoresis 2018; 39:1527-1542. [DOI: 10.1002/elps.201800029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/12/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Djuro Josić
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
- Department of Medicine; Brown Medical School; Brown University; Providence RI USA
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24
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Shen X, Sun L. Systematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics. Proteomics 2018; 18:e1700432. [PMID: 29577644 DOI: 10.1002/pmic.201700432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/02/2018] [Indexed: 11/08/2022]
Abstract
Immobilized trypsin (IM) has been recognized as an alternative to free trypsin (FT) for accelerating protein digestion 30 years ago. However, some questions of IM still need to be answered. How does the solid matrix of IM influence its preference for protein cleavage and how well can IM perform for deep bottom-up proteomics compared to FT? By analyzing Escherichia coli proteome samples digested with amine or carboxyl functionalized magnetic bead-based IM (IM-N or IM-C) or FT, it is observed that IM-N with the nearly neutral solid matrix, IM-C with the negatively charged solid matrix, and FT have similar cleavage preference considering the microenvironment surrounding the cleavage sites. IM-N (15 min) and FT (12 h) both approach 9000 protein identifications (IDs) from a mouse brain proteome. Compared to FT, IM-N has no bias in the digestion of proteins that are involved in various biological processes, are located in different components of cells, have diverse functions, and are expressed in varying abundance. A high-throughput bottom-up proteomics workflow comprising IM-N-based rapid protein cleavage and fast CZE-MS/MS enables the completion of protein sample preparation, CZE-MS/MS analysis, and data analysis in only 3 h, resulting in 1000 protein IDs from the mouse brain proteome.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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25
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Andjelković U, Tufegdžić S, Popović M. Use of monolithic supports for high-throughput protein and peptide separation in proteomics. Electrophoresis 2017; 38:2851-2869. [DOI: 10.1002/elps.201700260] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Uroš Andjelković
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
| | - Srdjan Tufegdžić
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
| | - Milica Popović
- Faculty of Chemistry; University of Belgrade; Belgrade Serbia
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26
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Yi L, Piehowski PD, Shi T, Smith RD, Qian WJ. Advances in microscale separations towards nanoproteomics applications. J Chromatogr A 2017; 1523:40-48. [PMID: 28765000 PMCID: PMC6042839 DOI: 10.1016/j.chroma.2017.07.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023]
Abstract
Microscale separation (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. In recent decades significant advances have been achieved in MS-based proteomics. However, the current proteomics platforms still face an analytical challenge in overall sensitivity towards nanoproteomics applications for starting materials of less than 1μg total proteins (e.g., cellular heterogeneity in tissue pathologies). Herein, we review recent advances in microscale separation techniques and integrated sample processing strategies that improve the overall sensitivity and proteome coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.
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Affiliation(s)
- Lian Yi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
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27
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Volokitina MV, Nikitina AV, Tennikova TB, Korzhikova-Vlakh EG. Immobilized enzyme reactors based on monoliths: Effect of pore size and enzyme loading on biocatalytic process. Electrophoresis 2017; 38:2931-2939. [DOI: 10.1002/elps.201700210] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 04/09/2017] [Accepted: 04/09/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Mariia V. Volokitina
- Russian Academy of Sciences; Institute of Macromolecular Compounds; St. Petersburg Russia
- Institute of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Anna V. Nikitina
- Institute of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Tatiana B. Tennikova
- Institute of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Evgenia G. Korzhikova-Vlakh
- Russian Academy of Sciences; Institute of Macromolecular Compounds; St. Petersburg Russia
- Institute of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
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28
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Brandtzaeg OK, Røen BT, Enger S, Lundanes E, Wilson SR. Multichannel Open Tubular Enzyme Reactor Online Coupled with Mass Spectrometry for Detecting Ricin. Anal Chem 2017; 89:8667-8673. [PMID: 28783436 DOI: 10.1021/acs.analchem.7b02590] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For counterterrorism purposes, a selective nano liquid chromatography-mass spectrometry (nanoLC-MS) platform was developed for detecting the highly lethal protein ricin from castor bean extract. Manual sample preparation steps were omitted by implementing a trypsin/Lys-C enzyme-immobilized multichannel reactor (MCR) consisting of 126 channels (8 μm inner diameter in all channels) that performed online digestion of proteins (5 min reaction time, instead of 4-16 h in previous in-solution methods). Reduction and alkylation steps were not required. The MCR allowed identification of ricin by signature peptides in all targeted mode injections performed, with a complete absence of carry-over in blank injections. The MCRs (interior volume ≈ 1 μL) have very low backpressure, allowing for trivial online coupling with commercial nanoLC-MS systems. The open tubular nature of the MCRs allowed for repeatable within/between-reactor preparation and performance.
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Affiliation(s)
| | - Bent-Tore Røen
- Norwegian Defence Research Establishment (FFI) , P.O. Box 25, N-2027 Kjeller, Norway
| | - Siri Enger
- Norwegian Defence Research Establishment (FFI) , P.O. Box 25, N-2027 Kjeller, Norway
| | - Elsa Lundanes
- Department of Chemistry, University of Oslo , P.O. Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Steven Ray Wilson
- Department of Chemistry, University of Oslo , P.O. Box 1033, Blindern, NO-0315 Oslo, Norway
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29
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Jiang X, Zhang D, Li X, Wang X, Bai L, Liu H, Yan H. Fabrication of a novel hemin-based monolithic column and its application in separation of protein from complex bio-matrix. J Pharm Biomed Anal 2017; 138:14-21. [DOI: 10.1016/j.jpba.2017.01.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/27/2016] [Accepted: 01/14/2017] [Indexed: 12/28/2022]
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30
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Yaprak E, Kasap M, Akpınar G, Kayaaltı-Yüksek S, Sinanoğlu A, Guzel N, Demirturk Kocasarac H. The prominent proteins expressed in healthy gingiva: a pilot exploratory tissue proteomics study. Odontology 2017; 106:19-28. [DOI: 10.1007/s10266-017-0302-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/09/2017] [Indexed: 12/31/2022]
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31
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Porous monoliths for on-line sample preparation: A review. Anal Chim Acta 2017; 964:24-44. [DOI: 10.1016/j.aca.2017.02.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 11/23/2022]
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32
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Shah V, Lassman ME, Chen Y, Zhou H, Laterza OF. Achieving efficient digestion faster with Flash Digest: potential alternative to multi-step detergent assisted in-solution digestion in quantitative proteomics experiments. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:193-199. [PMID: 27794205 DOI: 10.1002/rcm.7778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 10/10/2016] [Accepted: 10/27/2016] [Indexed: 05/21/2023]
Abstract
RATIONALE In quantitative analysis of protein biomarkers and therapeutic proteins by liquid chromatography/mass spectrometry (LC/MS), it is a preferred and well-established approach to digest with proteolytic enzymes to produce smaller peptide fragments which are more suitable for LC/MS analysis than the intact protein. In-solution digestion is one widely used method for protein digestion. Proteolytically resistant proteins often require digestion times that extend beyond normal working hours and prohibit same day analysis. We evaluated the performance of an immobilized enzyme reactor (IMER) to determine if this technology could reduce method development time, digestion time and increase throughput. METHODS We digested human plasma samples using a commercially available IMER, Flash Digest, and compared it to an in-solution digestion method for analysis of three different apolipoprotein biomarkers APOE, APOC2, and APOC3. The plasma digests were analyzed via LC/MS using electrospray ionization (ESI) and multiple reaction monitoring (MRM). Value assigned calibrators were selected over a relevant physiological concentration range for each protein of interest. Quality control samples (QCs) and 'unknown' human plasma samples were analyzed with both methods. RESULTS Flash Digest significantly reduced digestion time for APOC3, the most proteolytically resistant of the three proteins, to 30 min compared with overnight used with in-solution digestion. The Flash Digest achieved comparable digestion efficiency with minimal method development and reduced sample preparation time. Both methods showed linearity over a physiologically relevant concentration range. Precision was evaluated and a percentage coefficient of variance (% CV) less than 8% was obtained during intra-day reproducibility evaluation for all three apolipoproteins with Flash Digest. Concentrations observed for QCs and unknown samples using Flash Digest were comparable to the in-solution method. CONCLUSIONS An IMER such as Flash Digest may be a potential alternative to in-solution digestion to accelerate digestion of proteolytically resistant proteins in a quantitative proteomics experiments, reduce method development time and increase throughput. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Vinit Shah
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Michael E Lassman
- Translational Molecular Biomarkers, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Ying Chen
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Haihong Zhou
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Omar F Laterza
- Translational Molecular Biomarkers, Merck Research Laboratories, Kenilworth, NJ, USA
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33
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Eeltink S, Wouters S, Dores-Sousa JL, Svec F. Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides. J Chromatogr A 2017; 1498:8-21. [PMID: 28069168 DOI: 10.1016/j.chroma.2017.01.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/22/2016] [Accepted: 01/02/2017] [Indexed: 11/27/2022]
Abstract
This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown.
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Affiliation(s)
- Sebastiaan Eeltink
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Sam Wouters
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - José Luís Dores-Sousa
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Frantisek Svec
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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34
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Yan L, Qiao L, Ji J, Li Y, Yin X, Lin L, Liu X, Yao J, Wang Y, Liu B, Qian K, Liu B, Yang P. In-tip nanoreactors for cancer cells proteome profiling. Anal Chim Acta 2017; 949:43-52. [DOI: 10.1016/j.aca.2016.11.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/29/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022]
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35
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Piehowski PD, Zhao R, Moore RJ, Clair G, Ansong C. Quantitative Proteomic Analysis of Mass Limited Tissue Samples for Spatially Resolved Tissue Profiling. Methods Mol Biol 2017; 1788:269-277. [PMID: 28980276 DOI: 10.1007/7651_2017_78] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Traditionally, proteomic studies have been carried out on whole tissues or organs enabling the profiling of thousands of proteins within a single LC-MS analysis. A disadvantage of this approach is that proteomes generated from whole tissues are an "average" that represents a blend of cell types and distinct anatomical regions which can obscure important biological phenomena. Laser capture microdissection (LCM) is an elegant method that allows tissue features of interest, as small as a single cell, to be identified and isolated for downstream analysis. Herein we describe an approach that utilizes an immobilized enzyme reactor (IMER) coupled directly to nanoLC-MS/MS for highly sensitive, automated, quantitative proteomic analysis of the microscopic tissue specimens generated by LCM.
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Affiliation(s)
- Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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Moore S, Hess S, Jorgenson J. Characterization of an immobilized enzyme reactor for on-line protein digestion. J Chromatogr A 2016; 1476:1-8. [PMID: 27876348 PMCID: PMC5136339 DOI: 10.1016/j.chroma.2016.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/29/2016] [Accepted: 11/13/2016] [Indexed: 01/05/2023]
Abstract
Despite the developments for faster liquid chromatographic and mass spectral detection techniques, the standard in-solution protein digestion for proteomic analyses has remained relatively unchanged. The typical in-solution trypsin protein digestion is usually the slowest part of the workflow, albeit one of the most important. The development of a highly efficient immobilized enzyme reactor (IMER) with rapid performance for on-line protein digestion would greatly decrease the analysis time involved in a proteomic workflow. Presented here is the development of a silica based IMER for on-line protein digestion, which produced rapid digestions in the presence of organic mobile phase for both model proteins and a complex sample consisting of the insoluble portion of a yeast cell lysate. Protein sequence coverage and identifications evaluated between the IMER and in-solution digestions were comparable. Overall, for a yeast cell lysate with only a 10s volumetric residence time on-column, the IMER identified 507 proteins while the in-solution digestion identified 490. There were no significant differences observed based on identified protein's molecular weight or isoelectric point between the two digestion methods. Implementation of the IMER into the proteomic workflow provided similar protein identification results, automation for sample analysis, and reduced the analysis time by 15h.
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Affiliation(s)
- Stephanie Moore
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - Stephanie Hess
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - James Jorgenson
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States.
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Wang B, Shangguan L, Wang S, Zhang L, Zhang W, Liu F. Preparation and application of immobilized enzymatic reactors for consecutive digestion with two enzymes. J Chromatogr A 2016; 1477:22-29. [DOI: 10.1016/j.chroma.2016.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 11/26/2022]
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38
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Yin J, Xu T, Zhang N, Wang H. Three-Enzyme Cascade Bioreactor for Rapid Digestion of Genomic DNA into Single Nucleosides. Anal Chem 2016; 88:7730-7. [DOI: 10.1021/acs.analchem.6b01682] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Junfa Yin
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tian Xu
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Zhang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hailin Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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39
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Lanshoeft C, Heudi O, Cianférani S. SMART Digest™ compared with pellet digestion for analysis of human immunoglobulin G1 in rat serum by liquid chromatography tandem mass spectrometry. Anal Biochem 2016; 501:23-5. [DOI: 10.1016/j.ab.2016.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 01/03/2023]
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40
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Zhao Q, Fang F, Wu C, Wu Q, Liang Y, Liang Z, Zhang L, Zhang Y. imFASP: An integrated approach combining in-situ filter-aided sample pretreatment with microwave-assisted protein digestion for fast and efficient proteome sample preparation. Anal Chim Acta 2016; 912:58-64. [DOI: 10.1016/j.aca.2016.01.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 01/02/2023]
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41
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Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI, Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. Anal Chem 2015; 88:95-121. [PMID: 26558748 DOI: 10.1021/acs.analchem.5b04230] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Xu Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Amanda E Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Shelley Deeke
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Bo Xu
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Ming Wen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Kai Cheng
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Deeptee Seebun
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Alexandra Star
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
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