1
|
Zhang X, Chen J, Sheng X, Ding CF, Yan Y. Preparation and characterization of a biomimetic honeycomb cross-linked chitosan membrane and its application in the serum of gastric cancer patients. Int J Biol Macromol 2024; 279:135367. [PMID: 39244117 DOI: 10.1016/j.ijbiomac.2024.135367] [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: 06/20/2024] [Revised: 08/23/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]
Abstract
Chitosan, as a biological macromolecule with excellent biocompatibility, has great potential for application in immobilized metal affinity chromatography (IMAC) strategies. In-depth analysis of low-abundance phosphopeptides in organisms can help reveal the pathological mechanisms of diseases. Here, we developed an IMAC material based on a biomimetic honeycomb chitosan membrane. The material demonstrates excellent biocompatibility, good hydrophilicity, and strong metal chelating capacity, which collectively confer outstanding enrichment properties. The material has high sensitivity (0.05 fmol), great selectivity (1:2000), excellent cycling stability (at least 10 cycles) and acid-base stability. In addition, the material was employed in human serum, successfully enriching 129 phosphopeptides from the serum of gastric cancer patients and 146 phosphopeptides from healthy controls. Sequence logo suggests a potential association between gastric cancer and glutamine. Ultimately, an in-depth gene ontology analysis was carried out on the phosphopeptides that were enriched in the serum samples. Compared to normal controls, our results demonstrated dysregulated expression of biological process, cellular component, and molecular function in gastric cancer patients. This suggests that the disease involves, such as blood coagulation pathways, cholesterol metabolism, and heparin binding. All experimental outcomes converge to demonstrate the substantial promise of the material for applications within proteomics research.
Collapse
Affiliation(s)
- Xiaoya Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Jiakai Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Xiuqin Sheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Chuan-Fan Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China.
| | - Yinghua Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China.
| |
Collapse
|
2
|
Zhang X, Wang B, Luo Y, Ding CF, Yan Y. An amino-rich polymer-coated magnetic nanomaterial for ultra-rapid separation of phosphorylated peptides in the serum of Parkinson's disease patients. Anal Bioanal Chem 2024; 416:3361-3371. [PMID: 38607383 DOI: 10.1007/s00216-024-05287-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
The elucidation of disease pathogenesis can be achieved by analyzing the low-abundance phosphopeptides in organisms. Herein, we developed a novel and easy-to-prepare polymer-coated nanomaterial. By improving the hydrophilicity and spatial conformation of the material, we effectively enhanced the adsorption of phosphopeptides and demonstrated excellent enrichment properties. The material was able to successfully enrich the phosphopeptides in only 1 min. Meanwhile, the material has high selectivity (1:2000), good loading capacity (100 μg/mg), excellent sensitivity (0.5 fmol), and great acid and alkali resistance. In addition, the material was applied to real samples, and 70 phosphopeptides were enriched from the serum of Parkinson's disease (PD) patients and 67 phosphopeptides were enriched from the serum of normal controls. Sequences Logo showed that PD is probably associated with threonine, glutamate, serine, and glutamine. Finally, gene ontology (GO) analysis was performed on phosphopeptides enriched in PD patients' serum. The results showed that PD patients expressed abnormal expression of the cholesterol metabolic process and cell-matrix adhesion in the biological process (BP), endoplasmic reticulum and lipoprotein in the cellular component (CC), and heparin-binding, lipid-binding, and receptor-binding in the molecular function (MF) as compared with normal individuals. All the experiments indicate that the nanomaterials have great potential in proteomics studies.
Collapse
Affiliation(s)
- Xiaoya Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Bing Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yiting Luo
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China.
| |
Collapse
|
3
|
Wu C, Zhang S, Hou C, Byers S, Ma J. In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium(IV)-Grafted Mesoporous Silica Enrichment. Anal Chem 2024; 96:8254-8262. [PMID: 38728223 PMCID: PMC11140682 DOI: 10.1021/acs.analchem.3c02150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
Detection of endogenous peptides, especially those with modifications (such as phosphorylation) in biofluids, can serve as an indicator of intracellular pathophysiology. Although great progress has been made in phosphoproteomics in recent years, endogenous phosphopeptidomics has largely lagged behind. One main hurdle in endogenous phosphopeptidomics analysis is the coexistence of proteins and highly abundant nonmodified peptides in complex matrices. In this study, we developed an approach using zirconium(IV)-grafted mesoporous beads to enrich phosphopeptides, followed by analysis with a high resolution nanoRPLC-MS/MS system. The bifunctional material was first tested with digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. Given the size exclusion nature, the beads were directly applied for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphopeptide data set cataloged to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies of serum and other biofluid samples.
Collapse
Affiliation(s)
- Ci Wu
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, China
| | - Shen Zhang
- Clinical
Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha 410000, China
| | - Chunyan Hou
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| | - Stephen Byers
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| | - Junfeng Ma
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| |
Collapse
|
4
|
Huang X, Wang B, Zhai R, Ding CF, Fang X, Dai X, Yan Y. Boric acids decorated polymers with Au nanoparticle anchor assisted laser desorption/ionization for qualitive and quantitative analysis of hydroxytyrosol in red wines. Food Chem 2024; 437:137873. [PMID: 37918150 DOI: 10.1016/j.foodchem.2023.137873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Hydroxytyrosol possesses a variety of biological and pharmacological activities that are beneficial to human health. However, the methodologies for its detection always suffered from problems. In this work, the gold nanoparticle modified polymer decorated with boric acids (pMBA/VPBA@Au) was synthesized and used both as the adsorbent and matrix to enrich and ionize small molecule substances through surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS). The pMBA/VPBA@Au displayed a low detection limit (8 × 10-6 M) and high selectivity (1:100) for the enrichment of hydroxytyrosol, and the linear correlation curve between the concentration of hydroxytyrosol and the intensity of MS had a good correlation (10-4-10-2 M, R2 = 0.997). Additionally, the pMBA/VPBA@Au was used to quantify hydroxytyrosol in red wines, and the contents were 0.053-0.094 μg/mL. In general, a simple and novel method for the detection of hydroxytyrosol by SALDI-MS using boric acid functionalized polymer was developed for the first time, showing a good practical application value.
Collapse
Affiliation(s)
- Xiaohui Huang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Baichun Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Rui Zhai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, PR China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, PR China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, PR China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
5
|
Xu Q, Guo X, Wang S, Feng Q, Yan S, Yan Y. Combination of click chemistry and Schiff base reaction: Post-synthesis of covalent organic frameworks as an immobilized metal ion affinity chromatography platform for efficient capture of global phosphopeptides in serum with chronic obstructive pulmonary disease. J Sep Sci 2024; 47:e2300900. [PMID: 38356233 DOI: 10.1002/jssc.202300900] [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: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
Reasonable design and construction of functionalized materials are of great importance for the enrichment of global phosphopeptides. In this work, Ti4+ functionalized hydrophilic covalent organic frameworks by introducing glutathione (GSH) and 2,3,4-trihydroxy benzaldehyde (THBA) via click chemistry and Schiff base reaction (COF-V@GSH-THBA-Ti4+ ) was constructed and applied for selective enrichment of phosphopeptides in serum. Benefit from the high surface area, excellent hydrophilicity as well as regular mesoporous structure, COF-V@GSH-THBA-Ti4+ displayed high selectivity (molar ratio of 2000:1), low limit of detection (0.5 fmol), high load capacity (100.0 mg/g) and excellent size-exclusion effect (1:10000) for enrichment of phosphopeptides. For actual bio-sample analysis, 15 phosphopeptides assigned to 10 phosphoproteins with 16 phosphorylated sites and 33 phosphopeptides assigned to 25 phosphoproteins with 34 phosphorylated sites were detected from the serum of patients with chronic obstructive pulmonary disease (COPD), and normal controls. Biological processes and molecular functions analysis further disclosed the difference of serums with phosphoproteomics between COPD and normal controls.
Collapse
Affiliation(s)
- Qian Xu
- Tongji University School of Medicine, Shanghai, China
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Xiaoli Guo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Simeng Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Shi Yan
- Tongji University School of Medicine, Shanghai, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
6
|
Wang J, Zhang X, Yan Y, Xuan R. Facile preparation of nitrogen/titanium-rich porous organic polymers for specific enrichment of N-glycopeptides and phosphopeptides. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:695-703. [PMID: 38214200 DOI: 10.1039/d3ay02011h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The comprehensive investigation of protein phosphorylation and glycosylation aids in the discovery of novel biomarkers as well as the understanding of the pathophysiology of illness. In this work, a nitrogen/titanium-rich porous organic polymer was developed by copolymerizing carbohydrazide (CH) and 2,3-dihydroxyterephthalaldehyde (2,3-Dha) and modifying with Ti4+ (CH-Dha-Ti4+). The adequate nitrogen contributes to the enrichment of glycopeptides via HILIC, while titanium benefits from capturing phosphopeptides through IMAC. The proposed method exhibits excellent selectivity (1 : 1000, both for glycopeptides and phosphopeptides), LOD (for glycopeptides: 0.05 fmol μL-1, for phosphopeptides: 0.2 fmol), loading capacity (for glycopeptides: 100 mg g-1, for phosphopeptides: 125 mg g-1) and size-exclusion effect (1 : 10 000, both for glycopeptides and phosphopeptides). Furthermore, CH-Dha-Ti4+ was applied to capture glycopeptides and phosphopeptides from human serum; 205 glycopeptides and 45 phosphopeptides were detected in the serum of normal controls; and 294 glycopeptides and 63 phosphopeptides were found in the serum of uremia patients after being analyzed by nano LC-MS/MS. The discovered glycopeptides and phosphopeptides were involved in several molecular biological processes and activities, according to a gene ontology study.
Collapse
Affiliation(s)
- Jiayi Wang
- The First Affiliated Hospital of Ningbo University, Ningbo 315020, China.
- Health Science Center, Ningbo University, Ningbo 315211, China
| | - Xiaoya Zhang
- Health Science Center, Ningbo University, Ningbo 315211, China
| | - Yinghua Yan
- Health Science Center, Ningbo University, Ningbo 315211, China
| | - Rongrong Xuan
- The First Affiliated Hospital of Ningbo University, Ningbo 315020, China.
- Health Science Center, Ningbo University, Ningbo 315211, China
| |
Collapse
|
7
|
Hua S, Wang B, Ding CF, Yan Y. A novel carbon-based material with titanium and zirconium ions etched on hollow mesoporous carbon tubes for specific capture of phosphopeptides and exosomes. Talanta 2024; 266:125139. [PMID: 37659233 DOI: 10.1016/j.talanta.2023.125139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
The analysis of low abundance phosphopeptides in organisms and specific capture exosomes are crucial for unraveling the pathogenesis of diseases. For this reason, titanium-zirconium ions and highly biocompatible dopamine and polyimide tubes (PITs) were introduced, and a novel carbon-based material with titanium and zirconium ions etched on hollow mesoporous carbon tubes (HMCT), denoted as G@C@Ti-Zr-HMCT, comes into being after high-temperature calcination. Attributing to the tightly bound titanium and zirconium ions to HMCT and the high carbon content of the polydopamine carbonaceous layer, G@C@Ti-Zr-HMCT displays satisfactory capability of enriching phosphopeptides with satisfactory detection limit (0.2 fmol), extraordinary selectivity (1:2000), and good loading capacity (100 μg/mg). In addition, 25 phosphopeptides related to 25 phosphoproteins from the serum of Parkinson's disease (PD) patients and 30 phosphopeptides attributed to 26 phosphoproteins from the serum of healthy individuals were enriched by G@C@Ti-Zr-HMCT, respectively. In addition, bioinformatics analysis of the above results revealed that PD were associated with serine, threonine, and leucine of high frequency, blood coagulation in BP, Golgi apparatus and mitochondrial outer membrane in CC, and heparin binding in MF. Moreover, the phospholipid bilayer of exosomes and metallic titanium and zirconium ions interact to produce the following results: this highly biocompatible carbon-based material was successfully applied to capture exosomes, which offers a promising platform for isolating exosomes. To sum up, these delightful results confirmed without doubt that G@C@Ti-Zr-HMCT has enjoyed a splendiferous future in the specific capture of phosphopeptides and exosomes isolation.
Collapse
Affiliation(s)
- Shuwen Hua
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China
| | - Bing Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
8
|
Guo Y, Hua S, Wang B, Wang B, Ding CF, Yan Y. In situ grown magnetic COF@MOF with a phosphoserine anchor for in-depth N-glycopeptide analysis in serum. Analyst 2023; 148:5864-5872. [PMID: 37906056 DOI: 10.1039/d3an01473h] [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: 11/02/2023]
Abstract
A hydrophilic phosphoserine-functionalized magnetic organic framework composite (termed Fe3O4@COF@MOF-PS) was synthesized by an in situ growth strategy for effective capture of N-glycopeptides. Fe3O4@COF@MOF-PS exhibited high sensitivity (0.2 fmol μL-1), outstanding exclusion of size capability (1 : 10 000), good selectivity (1 : 2000), and reusability (at least 10 times). It also exhibited remarkable performance in the N-glycopeptide analysis in complex biological samples. Via nano-LC-MS/MS analysis, a total of 223 N-glycopeptides with 161 glycosylation sites assigned to 91 glycoproteins and 331 N-glycopeptides with 243 glycosylation sites assigned to 134 glycoproteins were identified in sera from cervical cancer patients and normal controls, respectively. Biological processes and molecular functional analyses indicate that the captured glycoproteins are of significant relevance to cervical cancer, for example, gene coverage or expression of cell adhesion and extracellular matrix structural constituents. Thus, Fe3O4@COF@MOF-PS not only efficiently captures N-glycopeptides, but also has the possibility of screening potential disease markers and elucidating the process of cervical cancer development.
Collapse
Affiliation(s)
- Yimin Guo
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Shuwen Hua
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Baichun Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Bing Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| |
Collapse
|
9
|
Prakasham K, Gurrani S, Shiea J, Wu MT, Singhania RR, Patel AK, Dong CD, Lin YC, Tsai B, Huang PC, Andaluri G, Ponnusamy VK. Facile analysis of mycotoxin in coffee and tea samples using a novel semi-automated in-syringe based fast mycotoxin extraction (FaMEx) technique coupled with direct-injection ESI-MS/MS analysis. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:1992-2000. [PMID: 37206414 PMCID: PMC10188741 DOI: 10.1007/s13197-023-05733-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 05/21/2023]
Abstract
Identifying the risk of ochratoxin A in our daily food has become fundamental because of its toxicity. In this work, we report a novel semi-automated in-syringe-based fast mycotoxin extraction (IS-FaMEx) technique coupled with direct-injection electrospray-ionization tandem mass spectrometer (ESI-MS/MS) detection for the quantification of ochratoxin A in coffee and tea samples. Under the optimized conditions, the results reveal that the developed method's linearity was more remarkable, with a correlation coefficient of > 0.999 and > 92% extraction recovery with a precision of 6%. The detection and quantification limits for ochratoxin A were 0.2 and 0.8 ng g-1 for the developed method, respectively, which is lower than the European Union regulatory limit of toxicity for ochratoxin-A (5 ng g-1) in coffee. Furthermore, the newly developed modified IS-FaMEx-ESI-MS/MS exhibited lower signal suppression of 8% with a good green metric score of 0.64. In addition, the IS-FaMEx-ESI-MS/MS showed good extraction recovery, matrix elimination, good detection, and quantification limits with high accuracy and precision due to the fewer extraction steps with semi-automation. Therefore, the presented method can be applied as a potential methodology for the detection of mycotoxins in food products for food safety and quality control purposes. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05733-z.
Collapse
Affiliation(s)
- Karthikeyan Prakasham
- PhD Program in Environmental and Occupational Medicine, & Research Center for Precision Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
| | - Swapnil Gurrani
- PhD Program in Environmental and Occupational Medicine, & Research Center for Precision Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
| | - Jentaie Shiea
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung City, 804 Taiwan
| | - Ming-Tsang Wu
- PhD Program in Environmental and Occupational Medicine, & Research Center for Precision Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
- Department of Public Health, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
| | - Reeta Rani Singhania
- PhD Program of Aquatic Science and Technology & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City, 81157 Taiwan
| | - Anil Kumar Patel
- PhD Program of Aquatic Science and Technology & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City, 81157 Taiwan
| | - Cheng-Di Dong
- PhD Program of Aquatic Science and Technology & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City, 81157 Taiwan
| | - Yu-Chia Lin
- Research and Development Division, Great Engineering Technology (GETECH) Corporation, No.392, Yucheng Rd., Zuoying District, Kaohsiung City, 813 Taiwan
| | - Bongee Tsai
- Research and Development Division, Great Engineering Technology (GETECH) Corporation, No.392, Yucheng Rd., Zuoying District, Kaohsiung City, 813 Taiwan
| | - Po-Chin Huang
- PhD Program in Environmental and Occupational Medicine, & Research Center for Precision Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
- National Institute of Environmental Health Sciences, National Health Research Institutes (NHRI), Miaoli County, 35053 Taiwan
| | - Gangadhar Andaluri
- Civil and Environmental Engineering Department, College of Engineering, Temple University, Philadelphia, USA
| | - Vinoth Kumar Ponnusamy
- PhD Program in Environmental and Occupational Medicine, & Research Center for Precision Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University (KMU), Kaohsiung City, 807 Taiwan
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung City, 804 Taiwan
- PhD Program of Aquatic Science and Technology & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City, 81157 Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, 807 Taiwan
| |
Collapse
|
10
|
Wang D, Feng Q, Luo Y, Wang W, Yan Y, Ding CF. Self-assembly of hydrazide-linked porous organic polymers rich in titanium for efficient enrichment of glycopeptides and phosphopeptides from human serum. Analyst 2023. [PMID: 37368458 DOI: 10.1039/d3an00709j] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
In this work, titanium-rich hydrazide-linked porous organic polymers (hydrazide-POPs-Ti4+) were synthesized using hydrazine, 2,3-dihydroxyterephthalaldehyde (DHTA) and trimethyl 1,3,5-benzenetricarboxylate (TP) as the ligands. Hydrazide-POPs-Ti4+ combined with HILIC and IMAC can be used for simultaneous enrichment of glycopeptides and phosphopeptides. The detection limit of this protocol is 0.1 fmol μL-1 for glycopeptides and 0.005 fmol μL-1 for phosphopeptides, and the selectivities are 1 : 1000 and 1 : 2000 for glycopeptides and phosphopeptides, respectively. For practical bio-sample analysis, 201 glycopeptides associated with 129 glycoproteins and 26 phosphopeptides associated with 21 phosphoproteins were selectively captured from healthy human serum, and 186 glycopeptides associated with 117 glycoproteins and 60 phosphopeptides associated with 50 phosphoproteins were enriched in the serum of breast cancer patients. Gene Ontology analysis indicated that the identified glycoproteins and phosphoproteins were linked to breast cancer, including the binding of complement component C1q and low-density lipoprotein particles, protein oxidation and complement activation, suggesting that these connected pathways are probably engaged in the disease pathology of breast cancer.
Collapse
Affiliation(s)
- Danni Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Yiting Luo
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Weimin Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| |
Collapse
|
11
|
Chen J, Wang B, Luo Y, Wang W, Ding CF, Yan Y. Facile preparation of porphyrin-based porous organic polymers for specific enrichment and isolation of phosphopeptides and phosphorylated exosomes. Talanta 2023; 264:124771. [PMID: 37311329 DOI: 10.1016/j.talanta.2023.124771] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
Exosomes, which can be used to investigate various disease processes, are novel disease markers that have been extensively studied in recent years. In this work, zirconium-rich porphyrin-based porous organic polymers (Imi-Pops-Zr) were synthesized by a facile and low-cost strategy for specific enrichment and isolation of phosphorylated peptides and exosomes. The proposed material demonstrates a low detection limit (0.5 fmol), a high selectivity (bovine serum albumin (BSA): β-casein = 1000:1), and a loading capability of 100 mg/g for phosphopeptides. For complex practical samples, after enrichment with Imi-Pops-Zr, 4 characteristic phosphopeptides from human serum, 20 and 12 phosphopeptides from human saliva and defatted milk were detected, respectively. Besides, 74 phosphorylated peptides with 67 phosphorylation sites belonging to 61 phosphoproteins and 67 phosphorylated peptides with 63 phosphorylation sites belonging to 65 phosphoproteins were detected from the serum of normal controls and uremic patients, respectively. Biological processes, cellular components and molecular functions revealed that interleukin-6, tumor necrosis factor, high density lipoprotein and proteases binding may be associated with uremia. Furthermore, Imi-Pops-Zr was successfully used to enrich and isolate exosomes from human serum. The experimental results show that Imi-Pops-Zr has promising application in the specific enrichment of phosphorylated peptides and exosomes in complex bio-samples.
Collapse
Affiliation(s)
- Jiakai Chen
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China
| | - Bing Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China
| | - Yiting Luo
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China
| | - Weimin Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
12
|
Li S, Wei Y, Wang Y, Liang H. Advances in hydrophilic metal-organic frameworks for N-linked glycopeptide enrichment. Front Chem 2022; 10:1091243. [PMID: 36531319 PMCID: PMC9751774 DOI: 10.3389/fchem.2022.1091243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 02/06/2024] Open
Abstract
The comprehensive profiling of glycoproteins is of great significance for the timely clinical diagnosis and therapy. However, inherent obstacles hamper their direct analysis from biological samples, and specific enrichment prior to analysis is indispensable. Among the various approaches for glycopeptide enrichment, hydrophilic interaction liquid chromatography (HILIC) has attracted special focus, especially for the development of novel hydrophilic materials, which is the key of HILIC. Metal-organic frameworks (MOFs) are a type of porous materials constructed from the self-assembly of metal and organic linkers. Advantages such as high surface area, flexible pore size, and easy modification render hydrophilic MOFs as ideal candidates for HILIC, which has inspired many studies over the past years. In this review, advances in hydrophilic MOFs for N-linked glycopeptide enrichment are summarized. According to the synthesis strategies, those materials are categorized into three classes, namely pristine MOFs, MOFs with chemical modifications, and MOFs-derived composite. In each categorization, the preparation and the function of different moieties are covered, as well as the enrichment performances of sensitivity, selectivity, and practical application. Finally, a summary and future perspective on the applications of hydrophilic MOFs for N-linked glycopeptide enrichment are briefly discussed. This review is expected to raise awareness of the properties of hydrophilic MOFs and offer some valuable information to further research in glycoproteomics.
Collapse
Affiliation(s)
| | | | | | - Haoran Liang
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
| |
Collapse
|
13
|
Adsorptive carbon-based materials for biomedical applications. ENGINEERED REGENERATION 2022. [DOI: 10.1016/j.engreg.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
14
|
Xie Z, Feng Q, Zhang S, Yan Y, Deng C, Ding CF. Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis. Proteomics 2022; 22:e2200070. [PMID: 36100958 DOI: 10.1002/pmic.202200070] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/06/2022] [Accepted: 08/15/2022] [Indexed: 11/08/2022]
Abstract
As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.
Collapse
Affiliation(s)
- Zehu Xie
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Shun Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Chunhui Deng
- Department of Chemistry, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| |
Collapse
|
15
|
Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
16
|
Jiang Y, Liang W, Wang B, Feng Q, Xia C, Wang Q, Yan Y, Zhao L, Cui W, Liang H. Magnetic mesoporous silica nanoparticles modified by phosphonate functionalized ionic liquid for selective enrichment of phosphopeptides. RSC Adv 2022; 12:26859-26865. [PMID: 36320858 PMCID: PMC9490807 DOI: 10.1039/d2ra04609a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
In this study, new magnetic nanoparticles (denotated as Fe3O4@mSiO2-PFIL-Ti4+) have been prepared by immobilizing titanium ions with phosphonate functionalized ionic liquid (PFIL) on the wall of core-shell structured mesoporous nanomaterials. The resulting nanoparticles possess large specific surface area, strong hydrophilicity and fast magnetic response. The composites can capture traces of phosphopeptides from the tryptic β-casein digest (0.08 fmol), a digest mixture of β-casein and BSA (1 : 10 000, molar ratio) as well as a blend of β-casein digest and a great quantity of phosphorylated protein (β-casein) and non-phosphorylated protein (BSA) (1 : 2000 : 2000, mass ratio), respectively, showing excellent sensitivity, selectivity and size exclusion ability. Additionally, Fe3O4@mSiO2-PFIL-Ti4+ shows excellent steadiness and can be reused at least 12 times. Moreover, this material was successfully applied to enrich endogenous phosphopeptides from complex bio-samples, including human saliva and serum.
Collapse
Affiliation(s)
- Yufei Jiang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| | - Weida Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| | - Binbin Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| | - Chenglong Xia
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| | - Qiyao Wang
- Ningbo Key Laboratory of Behaviour Neuroscience, Zhejiang Province Key Laboratory of Pathophysiology, School of Medicine, Ningbo University Ningbo 315211 China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| | - Lingling Zhao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| | - Wei Cui
- Ningbo Key Laboratory of Behaviour Neuroscience, Zhejiang Province Key Laboratory of Pathophysiology, School of Medicine, Ningbo University Ningbo 315211 China
| | - Hongze Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University Ningbo 315211 China
| |
Collapse
|
17
|
Wu Y, Chen H, Chen Y, Sun N, Deng C. Metal organic frameworks as advanced extraction adsorbents for separation and analysis in proteomics and environmental research. Sci China Chem 2022. [DOI: 10.1007/s11426-021-1195-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
18
|
Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
|
19
|
Jiang-Long DU, Meng-Yao FU, Ying-Hua YAN, Chuan-Fan DING. A complementary bimetal synergized with polyethyleneimine functionalized affinity chromatography nanosphere for enrichment of global phosphopeptides. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2021.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
20
|
Li Y, Li H, Xie Y, Chen S, Qin R, Dong H, Yu Y, Wang J, Qian X, Qin W. An Integrated Strategy for Mass Spectrometry-Based Multiomics Analysis of Single Cells. Anal Chem 2021; 93:14059-14067. [PMID: 34643370 DOI: 10.1021/acs.analchem.0c05209] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-cell-based genomics and transcriptomics analysis have revealed substantial cellular heterogeneity among seemingly identical cells. Knowledge of the cellular heterogeneity at multiomics levels is vital for a better understanding of tumor metastasis and drug resistance, stem cell differentiation, and embryonic development. However, unlike genomics and transcriptomics studies, single-cell characterization of metabolites, proteins, and post-translational modifications at the omics level remains challenging due to the lack of amplification methods and the wide diversity of these biomolecules. Therefore, new tools that are capable of investigating these unamplifiable "omes" from the same single cells are in high demand. In this work, a microwell chip was prepared and the internal surface was modified for hydrophilic interaction liquid chromatography-based tandem extraction of metabolites and proteins and subsequent protein digestion. Next, direct electrospray ionization mass spectrometry was adopted for single-cell metabolome identification, and a data-independent acquisition-mass spectrometry approach was established for simultaneous proteome profiling and phosphoproteome analysis without phosphopeptide enrichment. This integrated strategy resulted in 132 putatively annotated compounds, more than 1200 proteins, and the first large-scale phosphorylation data set from single-cell analysis. Application of this strategy in chemical perturbation studies provides a multiomics view of cellular changes, demonstrating its capability for more comprehensive investigation of cellular heterogeneity.
Collapse
Affiliation(s)
- Yuanyuan Li
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Hang Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yuping Xie
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Shuo Chen
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Ritian Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Hangyan Dong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yongliang Yu
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Jianhua Wang
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,College of Basic Medicine, Anhui Medical University, Hefei 230032, P. R. China
| |
Collapse
|
21
|
Pasquardini L, Bossi AM. Molecularly imprinted polymers by epitope imprinting: a journey from molecular interactions to the available bioinformatics resources to scout for epitope templates. Anal Bioanal Chem 2021; 413:6101-6115. [PMID: 34018035 PMCID: PMC8440283 DOI: 10.1007/s00216-021-03409-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023]
Abstract
The molecular imprinting of proteins is the process of forming biomimetics with entailed protein-recognition by means of a template-assisted synthesis. Protein-imprinted polymers (pMIPs) have been successfully employed in separations, assays, sensors, and imaging. From a technical point of view, imprinting a protein is both costly, for protein expression and purification, and challenging, for the preservation of the protein's structural properties. In fact, the imprinting process needs to guarantee the preservation of the same protein three-dimensional conformation that later would be recognized. So far, the captivating idea to imprint just a portion of the protein, i.e., an epitope, instead of the whole, proved successful, offering reduced costs, compatibility with many synthetic conditions (solvents, pH, temperatures), and fine-tuning of the peptide sequence so to target specific physiological and functional conditions of the protein, such as post-translational modifications. Here, protein-protein interactions and the biochemical features of the epitopes are inspected, deriving lessons to prepare more effective pMIPs. Epitopes are categorized in linear or structured, immunogenic or not, located at the protein's surface or buried in its core and the imprinting strategies are discussed. Moreover, attention is given to freely available online bioinformatics resources that might offer key tools to gain further rationale amid the selection process of suitable epitopes templates.
Collapse
Affiliation(s)
| | - Alessandra Maria Bossi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| |
Collapse
|
22
|
Chen C, Zhang X, Dong X, Zhou H, Li X, Liang X. TiO 2 Simultaneous Enrichment, On-Line Deglycosylation, and Sequential Analysis of Glyco- and Phosphopeptides. Front Chem 2021; 9:703176. [PMID: 34458235 PMCID: PMC8385670 DOI: 10.3389/fchem.2021.703176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
Reversible protein glycosylation and phosphorylation tightly modulate important cellular processes and are closely involved in pathological processes in a crosstalk dependent manner. Because of their significance and low abundances of glyco- and phosphopeptides, several strategies have been developed to simultaneously enrich and co-elute glyco- and phosphopeptides. However, the co-existence of deglycosylated peptides and phosphopeptides aggravates the mass spectrometry analysis. Herein we developed a novel strategy to analyze glyco- and phosphopeptides based on simultaneous enrichment with TiO2, on-line deglycosylation and collection of deglycosylated peptides, and subsequent elution of phosphopeptides. To optimize on-line deglycosylation conditions, the solution pH, buffer types and concentrations, and deglycosylation time were investigated. The application of this novel strategy to 100 μg mouse brain resulted in 355 glycopeptides and 1,975 phosphopeptides, which were 2.5 and 1.4 folds of those enriched with the reported method. This study will expand the application of TiO2 and may shed light on simultaneously monitoring protein multiple post-translational modifications.
Collapse
Affiliation(s)
- Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xuefang Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Han Zhou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| |
Collapse
|
23
|
Xu H, Zhang Z, Wang Y, Lu W, Min Q. Engineering of nanomaterials for mass spectrometry analysis of biomolecules. Analyst 2021; 146:5779-5799. [PMID: 34397044 DOI: 10.1039/d1an00860a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) based analysis has received intense attention in diverse biological fields. However, direct MS interrogation of target biomolecules in complex biological samples is still challenging, due to the extremely low abundance and poor ionization potency of target biological species. Innovations in nanomaterials create new auxiliary tools for deep and comprehensive MS characterization of biomolecules. More recently, growing research interest has been directed to the compositional and structural engineering of nanomaterials for enriching target biomolecules prior to MS analysis, enhancing the ionization efficiency in MS detection and designing biosensing nanoprobes in sensitive MS readout. In this review, we mainly focus on the recent advances in the engineering of nanomaterials towards their applications in sample pre-treatment, desorption/ionization matrices and ion signal amplification for MS profiling of biomolecules. This review will provide a toolbox of nanomaterials for researchers devoted to developing analytical methods and practical applications in the biological MS field.
Collapse
Affiliation(s)
- Hongmei Xu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China. and Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Yihan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Weifeng Lu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| |
Collapse
|
24
|
FENG J, JI X, LI C, SUN M, HAN S, FENG J, SUN H, FENG Y, SUN M. [Recent advance of new sample preparation materials in the analysis and detection of environmental pollutants]. Se Pu 2021; 39:781-801. [PMID: 34212580 PMCID: PMC9404022 DOI: 10.3724/sp.j.1123.2021.02030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Indexed: 11/25/2022] Open
Abstract
To successfully analyze complex samples and detect trace targets, sample pretreatment is essential. Efficient sample pretreatment techniques can remove or reduce interference from the sample matrix. It can also enrich analytes, thereby improving analytical accuracy and sensitivity. In recent years, various sample preparation techniques, including SPE, magnetic dispersion SPE, pipette tip SPE, stir bar extraction, fiber SPME, and in-tube SPME, have received increasing attention in environmental analysis and monitoring. The extraction efficiency mainly depends on the type of adsorbent material. Therefore, the development of efficient adsorbents is a crucial step toward sample preparation. This review summarizes and discusses the research advances in extraction materials over recent years. These extraction materials contain inorganic adsorbents, organic adsorbents, and inorganic-organic hybrid materials such as graphene, graphene oxide, carbon nanotubes, inorganic aerogels, organic aerogels, triazinyl-functionalized materials, triazine-based polymers, molecularly imprinted polymers, covalent organic frameworks, metal-organic frameworks, and their derivatives. These materials have been applied to extract different types of pollutants, including metal ions, polycyclic aromatic hydrocarbons, plasticizers, alkanes, phenols, chlorophenols, chlorobenzenes, polybrominated diphenyl ethers, perfluorosulfonic acids, perfluorocarboxylic acids, estrogens, drug residues, and pesticide residues, from environmental samples (such as water and soil samples). These sample preparation materials possess high surface areas, numerous adsorption sites, and allow extraction via various mechanisms, such as π-π, electrostatic, hydrophobic, and hydrophilic interactions, as well as hydrogen and halogen bond formation. Various sample pretreatment techniques based on these extraction materials have been combined with various detection methods, including chromatography, mass spectrometry, atomic absorption spectroscopy, fluorescence spectroscopy, and ion mobility spectroscopy, and have been extensively used for the determination of environmental pollutants. The existing challenges associated with the development of sample preparation techniques are proposed, and prospects for such extraction materials in environmental analysis and monitoring are discussed. Major trends in the field, including the development of efficient extraction materials with high enrichment ability, good selectivity, excellent thermal stability, and chemical stability, are discussed. Green sample pretreatment materials, environmentally friendly synthesis methods, and green sample pretreatment methods are also explored. Rapid sample pretreatment methods that can be conducted within minutes or seconds are of significant interest. Further, online sample pretreatment and automatic analysis methods have attracted increasing attention. Besides, real-time analysis and in situ detection have been important development directions, and are expected to be widely applicable in environmental analysis, biological detection, and other fields. Modern synthesis technology should be introduced to synthesize specific extraction materials. Controllable preparation methods for extraction materials, such as the in situ growth or in situ preparation of extraction coatings, will acquire importance in coming years. It will also be important to adopt high-performance materials from other fields for sample pretreatment. Organic-inorganic hybrid extraction materials can combine the advantages both organic materials and inorganic materials, and mutually compensate for any disadvantages. Extraction materials doped with nanomaterials are also promising. Although existing sample pretreatment techniques are relatively efficient, it is still imperative to develop novel sample preparation methods.
Collapse
Affiliation(s)
- Juanjuan FENG
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Xiangping JI
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Chunying LI
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Mingxia SUN
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Sen HAN
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Jiaqing FENG
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Haili SUN
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yang FENG
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Min SUN
- 济南大学化学化工学院, 山东 济南 250022
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| |
Collapse
|
25
|
Fang X, Liu X, Sun N, Deng C. Enhanced specificity of bimetallic ions via mesoporous confinement for phosphopeptides in human saliva. Talanta 2021; 233:122587. [PMID: 34215077 DOI: 10.1016/j.talanta.2021.122587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 11/17/2022]
Abstract
Phosphopeptides were of great significance in disease diagnosis and monitoring its dynamic changes. In this article, we proposed a more efficient method to synthesize a kind of bimetallic mesoporous silica nanomaterials (Fe3O4@mSiO2-PO3-Ti4+/Zr4+) and applied it to the analysis of phosphopeptides in human saliva samples based on IMAC technology. The chelation group was introduced into mesopores at the same time as the formation of mesoporous silica which significantly reduced the synthesis procedure and improved the synthesis efficiency. The as-prepared materials showed great sensitivity, selectivity and size-exclusion performance for phosphopeptides in standard β-casein digests. More importantly, the materials identified 85 phosphopeptides in disease saliva samples which provided a candidate choice in future clinical examination.
Collapse
Affiliation(s)
- Xiaowei Fang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Xingang Liu
- Center of Analysis and Measurement, Fudan University, Shanghai, 200438, China.
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Chunhui Deng
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China; Department of Chemistry, Fudan University, Shanghai, 200438, China.
| |
Collapse
|
26
|
Yan Y, Han R, Hou Y, Zhang H, Yu J, Gao W, Xu L, Tang K. Bowl-like mesoporous polydopamine with size exclusion for highly selective recognition of endogenous glycopeptides. Talanta 2021; 233:122468. [PMID: 34215103 DOI: 10.1016/j.talanta.2021.122468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 01/01/2023]
Abstract
It has been confirmed that endogenous glycopeptide plays an important role in a variety of pathological and physiological processes. However, direct analysis of endogenous glycopeptide is still a great challenge owing to the low abundance of endogenous glycopeptides and the presence of a large number of interfering substances such as large-sized proteins and heteropeptides in complex biological sample. Herein, we reported a novel bowl-like mesoporous polydopamine nanoparticle modified by carrageenan (denoted as MPDA@PEI@CA) with strong hydrophilicity and size-exclusion effect for high specificity enrichment of endogenous glycopeptides. Thanks to the suitable pore channel structure as well as strong hydrophilic surface, the as-prepared MPDA@PEI@CA nanoparticles exhibited prominent performance in enrichment of N-linked glycopeptide with ultrahigh selectivity (1:5000 M ratio of horseradish peroxidase (HRP) digests/bovine serum albumin (BSA) digests), low detection limit (5 fmol μL-1), outstanding size-exclusion ability (1:1000 mass of HRP/BSA), and unique reusability (five times). 125 N-glycosylation sites of 134 glycopeptides from 65 glycoproteins were identified from 2 μL sample of human serum treated with the MPDA@PEI@CA nanoparticles, which manifested the ability to enrich endogenous N-linked glycopeptides from complex biological samples. These results indicated that the bowl-like MPDA@PEI@CA nanoparticles with novel structure prepared in this work had great potential for glycopeptidome analysis.
Collapse
Affiliation(s)
- Yuyan Yan
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Renlu Han
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| | - Yafei Hou
- Department of Microelectronic Science and Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Huijun Zhang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Jiancheng Yu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, PR China
| | - Wenqing Gao
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Long Xu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Keqi Tang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, PR China; Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| |
Collapse
|
27
|
Xu W, Cao JF, Lin YN, Shu Y, Wang JH. Functionalized polyoxometalate microspheres ensure selective adsorption of phosphoproteins and glycoproteins. Chem Commun (Camb) 2021; 57:3367-3370. [PMID: 33683273 DOI: 10.1039/d1cc00325a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lacunary polyoxometalate (POM), [PW9O34]9-, grafts with a boronic acid group attached via an organosilane bridge assemble into microspheres, PW9-Si-APBA. The oxygen-rich and hydrophilic surface of POM facilitates the binding of phosphate groups in phosphoproteins and glycans in glycoproteins. While the metal-oxo in POM provides π-π interactions with the phosphate groups of phosphoproteins, the boronic acid group specifically binds to glycoproteins via the cis-diols of glycans. Therefore, these multi-driving forces ensure the selective adsorption of phosphoproteins and glycoproteins by PW9-Si-APBA microspheres in biological sample matrixes, even in the presence of very high protein abundance, i.e., BSA, at mass ratio of β-ca/IgG/OVA/BSA = 1 : 1 : 1 : 200.
Collapse
Affiliation(s)
- Wang Xu
- Department of Chemistry, Northeastern University, Box 332, Shenyang 110819, China.
| | | | | | | | | |
Collapse
|
28
|
Du J, Yan Y, Tang K, Ding C. Modified Carbon Nanotubes Decorated with ZIFs as New Immobilized Metal Ion Affinity Chromatography Platform for Enrichment of Phosphopeptides. ChemistrySelect 2021. [DOI: 10.1002/slct.202004650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jianglong Du
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
| | - Yinghua Yan
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
| | - Keqi Tang
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
| | - Chuan‐Fan Ding
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
| |
Collapse
|
29
|
Hashemi SH, Kaykhaii M. Nanoparticle coatings for stir bar sorptive extraction, synthesis, characterization and application. Talanta 2021; 221:121568. [PMID: 33076116 DOI: 10.1016/j.talanta.2020.121568] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022]
Abstract
During the last ten years, number of articles published on synthesis and applications of nano-particles (NPs) have been increased by a factor of 40. One of the most interesting applications of NPs is their using as high capacity, robust and highly selective coatings for stir bar sorption extraction (SBSE). Utilizing NPs greatly promoted applications of SBSE and has gained importance on green sample preparation. In this article, all available literature on nano-coatings as media for microextraction by stir bar is reviewed. This includes non-functionalized NPs (mostly, metallic/metallic oxide and graphene based), functionalized coatings, and decorated coatings (both mono- and multifunctional). Various applications, advantages and disadvantages of each nano-coated prepared stir bar are discussed in detail along with critical evaluation of currently available methods.
Collapse
Affiliation(s)
- Sayyed Hossein Hashemi
- Department of Marine Chemistry, Faculty of Marine Science, Chabahar Maritime University, 98617-85553, Chabahar, Iran.
| | - Massoud Kaykhaii
- Department of Chemistry, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
| |
Collapse
|
30
|
Zhang H, Deng Y, Liu X, Sun J, Ma L, Ding Y, Zhan Z, Zhang H, Yang Y, Gu Y, Iliuk AB, Yang C, Tao WA. Glass Fiber-Supported Hybrid Monolithic Spin Tip for Enrichment of Phosphopeptides from Urinary Extracellular Vesicles. Anal Chem 2020; 92:14790-14797. [PMID: 33074658 PMCID: PMC8281360 DOI: 10.1021/acs.analchem.0c03557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extracellular vesicles (EVs) are attracting increasing interest with their intriguing role in intercellular communications. Protein phosphorylation in EVs is of great importance for understanding intercellular signaling processes. However, the study of EV phosphoproteomics is impeded by their relatively low amount in limited clinical sample volumes, and it is necessary to have a sensitive and efficient enrichment method for EV phosphopeptides. Herein, a novel Ti(IV)-functionalized and glass fiber-supported hybrid monolithic spin tip, termed PhosTip, was prepared for enriching phosphopeptides from urinary EVs. Glass fiber as the stationary phase positions the hybrid monolith in a standard pipet tip and prevents the monolith from distortion during experiments. The preparation procedure for the new PhosTip is simple and time-saving. The hybrid monolithic PhosTip provides excellent enrichment efficiency of low-abundance phosphopeptides from cell digests and urinary EVs with minimum contamination and sample loss. Using the PhosTip, we demonstrate that 5373 and 336 unique phosphopeptides were identified from 100 and 1 μg of cell lysates, while 3919 and 217 unique phosphopeptides were successfully identified from 10 and 1 mL of urinary samples, respectively. The PhosTip was finally applied to enrich phosphopeptides in urine EVs from prostate cancer patients and healthy controls and quantify 118 up-regulated proteins with phosphosites in prostate cancer samples. These results demonstrated that the PhosTip could be a simple and convenient tool for enriching phosphopeptides from clinical samples and for broader applications in biomarker discovery.
Collapse
Affiliation(s)
- Haiyang Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Yuanyuan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Xinyi Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Jie Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Leyao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Yajie Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Zhen Zhan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Hao Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Yuchen Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, No. 68, Changle Road, Nanjing 210009, China
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, No. 68, Changle Road, Nanjing 210009, China
| | - Anton B Iliuk
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chenxi Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center of Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
31
|
Liu Y, Xia C, Fan Z, Jiao F, Gao F, Xie Y, He Z, Zhang W, Zhang Y, Shen Y, Qian X, Qin W. Novel Two-Dimensional MoS 2-Ti 4+ Nanomaterial for Efficient Enrichment of Phosphopeptides and Large-Scale Identification of Histidine Phosphorylation by Mass Spectrometry. Anal Chem 2020; 92:12801-12808. [PMID: 32966065 DOI: 10.1021/acs.analchem.0c00618] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Due to its key roles in regulating the occurrence and development of cancer, protein histidine phosphorylation has been increasingly recognized as an important form of post-translational modification in recent years. However, large-scale analysis of histidine phosphorylation is much more challenging than that of serine/threonine or tyrosine phosphorylation, mainly because of its acid lability. In this study, MoS2-Ti4+ nanomaterials were synthesized using a solvothermal method and taking advantage of the electrostatic adsorption between MoS2 nanosheets and Ti4+. The MoS2-Ti4+ nanomaterials have the advantage of the combined affinity of Ti4+ and Mo toward phosphorylation under medium acidic conditions (pH = 3), which is crucial for preventing hydrolysis and loss of histidine phosphorylation during enrichment. The feasibility of using the MoS2-Ti4+ nanomaterial for phosphopeptide enrichment was demonstrated using mixtures of β-casein and bovine serum albumin (BSA). Further evaluation revealed that the MoS2-Ti4+ nanomaterial is capable of enriching synthetic histidine phosphopeptides from 1000 times excess tryptic-digested HeLa cell lysate. Application of the MoS2-Ti4+ nanomaterials for large-scale phosphopeptide enrichment results in the identification of 10 345 serine, threonine, and tyrosine phosphosites and the successful mapping of 159 histidine phosphosites in HeLa cell lysates, therefore indicating great potential for deciphering the vital biological roles of protein (histidine) phosphorylation.
Collapse
Affiliation(s)
- Yuanyuan Liu
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130118, China.,State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Chaoshuang Xia
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China.,Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Zhiya Fan
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Fenglong Jiao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Fangyuan Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yuping Xie
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Zhongmei He
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130118, China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yehua Shen
- Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Weijie Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| |
Collapse
|
32
|
Pu C, Zhao H, Gu Q, Zheng Y, Lan M. Targeted immobilization of titanium (IV) on magnetic mesoporous nanomaterials derived from metal-organic frameworks for high-efficiency phosphopeptide enrichment in biological samples. Mikrochim Acta 2020; 187:568. [PMID: 32929585 DOI: 10.1007/s00604-020-04556-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/07/2020] [Indexed: 10/24/2022]
Abstract
A selectively modified porous metal/carbon nanocomposite was fabricated to enhance the enrichment of low-abundance phosphopeptides from biological samples. The carbon matrix derived from the metal-organic framework provides a suitable pore size to allow the diffusion of peptides, while the deliberately modified metal nanoparticles within the pores enhance their interaction with the phosphopeptides. This nanocomposite shows extremely high enrichment selectivity for phosphopeptides in the MALDI-TOF MS detection, even when the molar ratio of α-casein digests versus bovine serum albumin digests was up to about 1:20,000. By combining such nanocomposite with nano-LC-MS/MS, 4556 unique phosphopeptides were identified with high selectivity (95.2%) from HeLa cell extracts. Furthermore, phosphopeptides from prostate tissue digests were also determined. A total of 277 and 1242 phosphopeptides were identified from normal and tumor tissues of a patient with prostate cancer, respectively. This indicates that phosphorylation and prostate cancer can be related to each other.
Collapse
Affiliation(s)
- Chenlu Pu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Qinying Gu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Yu Zheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China. .,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| |
Collapse
|
33
|
Büyüktiryaki S, Keçili R, Hussain CM. Functionalized nanomaterials in dispersive solid phase extraction: Advances & prospects. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115893] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|