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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.
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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
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2
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Cerrato A, Cavaliere C, Montone CM, Piovesana S. New hydrophilic material based on hydrogel polymer for the selective enrichment of intact glycopeptides from serum protein digests. Anal Chim Acta 2023; 1245:340862. [PMID: 36737137 DOI: 10.1016/j.aca.2023.340862] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
The paper describes the preparation and characterization of a new HILIC material for the enrichment of N-linked glycopeptides. The material was prepared using 2-acrylamido-2-methyl-1-propanesulfonic acid as the monomer and ethylene glycol dimethacrylate as the cross-linker. The material was developed by a Box-Behnken experimental design, taking into consideration the amount of monomer-to-crosslinker ratio, the composition, and the amount of porogen mixture. By this approach, the property of the resulting polymer could be fine-tuned to modulate the hydrophilicity and porosity. As HILIC enrichment is mostly dependent on hydrophilic interactions, including H-bonding, the amount of swelling was expected to have an important function, therefore the optimization considered a monomer percent in the range of 20-80%, which implied very different water swelling capacities. After assessing the potential of this new polymer family on fetuin digests, the 17 materials resulting from the Box-Behnken experimental design were used for the enrichment of glycopeptides from serum protein digests. The materials displayed a superior performance over cotton HILIC enrichment, both in terms of the number of enriched N-linked glycopeptides and selectivity, providing up to 762 N-linked glycopeptides with 77% selectivity. The optimization indicated that a high amount of monomer significantly affected the number of enriched glycopeptides, which is also closely connected with the hydrogel nature of the resulting polymers. The results not only provide one additional HILIC material for the enrichment of glycopeptides but also pave the way for the use and development of hydrogel materials for the enrichment of N-linked glycopeptides.
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Affiliation(s)
- Andrea Cerrato
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Susy Piovesana
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
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3
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Irfan A, Feng W, Liu K, Habib K, Qu Q, Yang L. TiO 2-modified fibrous core-shell mesoporous material to selectively enrich endogenous phosphopeptides with proteins exclusion prior to CE-MS analysis. Talanta 2021; 235:122737. [PMID: 34517605 DOI: 10.1016/j.talanta.2021.122737] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 02/01/2023]
Abstract
As an important post-translational modification of proteins, phosphorylation plays a key role in regulating a variety of complicated biological reactions. Owing to the fact that phosphopeptides are low abundant and the ionization efficiency could be suppressed in mass spectroscopic detection, highly efficient and selective enrichment methods are essential to identify protein phosphorylation by mass spectrometry. Here, we develop novel titanium oxide coated core shell mesoporous silica (CSMS@TiO2) nanocomposites for enrichment of phosphopeptides with simultaneous exclusion of massive proteins. The CSMS@TiO2 nanocomposites have essential features, including uniform 1.0 μm diameter, 120 nm thick shell, 7.0 nm mesopores perpendicular to the surface, large surface area of 77 m2/g and pore volume of 0.15 cm3/g, therefore can greatly improve the sensitivity for identifying phosphopeptides by capillary electrophoresis-mass spectrometry. The proposed CSMS@TiO2 nanocomposites are applied for analysis of β-casein tryptic digest and bovine serum albumin (BSA) protein mixture, respectively. The results show that the number of phosphopeptides detected is tremendously increased by using CSMS@TiO2 nanocomposite, proving selectively enriching phosphopeptides due to the size-exclusive and specific interaction of the TiO2-modified mesopores. The enrichment of the phosphopeptides is achieved even for the digests at very low concentration of β-casein (1 fmol/μL). This research would open up a promising idea to utilize mesoporous materials in peptidomics analysis.
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Affiliation(s)
- Azhar Irfan
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Wenxia Feng
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Kexin Liu
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Khan Habib
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Qishu Qu
- Key Laboratory of Functional Molecule Design and Interface Process, School of Materials and Chemical Engineering, Anhui Jianzhu University, Hefei, Anhui Province, 230601, China.
| | - Li Yang
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China.
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4
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Poly amidoamine functionalized poly (styrene-divinylbenzene-glycidylmethacrylate) composites for the rapid enrichment and determination of N-phosphoryl peptides. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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5
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Hydrophilic polydopamine-derived mesoporous channels for loading Ti(IV) ions for salivary phosphoproteome research. Anal Chim Acta 2020; 1146:53-60. [PMID: 33461719 DOI: 10.1016/j.aca.2020.12.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/21/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022]
Abstract
Salivary phosphoproteome holds great promise in clinic diagnosis. For profiling of salivary phosphoproteome, it is essential to develop efficient enrichment methods prior to mass spectrum (MS). Among developed enrichment strategies, immobilized metal ions affinity chromatography (IMAC) has exhibited outstanding performance. In this work, we report a coherent approach where polydopamine (PDA) is first utilized to form mesoporous structure through soft templating method, then chelated with Ti4+ to construct hydrophilic polydopamine-derived magnetic mesoporous nanocomposite (denoted Fe3O4@mPDA@Ti4+). In virtue of the merits including ordered mesoporous channels, appropriate superparamagnetism, and abundant Ti4+, the enrichment strategy based on Fe3O4@mPDA@Ti4+ combined with MS is employed for accurate identification of phosphopeptides in β-casein digest and human saliva. As expected, Fe3O4@mPDA@Ti4+ revealed a great selectivity (1:200) and a low detection limit (0.1 fmol μL-1) toward phosphopeptides. More importantly, the further successful capture of phosphopeptides from human saliva indicated the prominent potential of this method for seeking phosphopeptide biomarkers in further analysis.
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Sürmen MG, Sürmen S, Ali A, Musharraf SG, Emekli N. Phosphoproteomic strategies in cancer research: a minireview. Analyst 2020; 145:7125-7149. [PMID: 32996481 DOI: 10.1039/d0an00915f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into cancer mechanisms and aid in the diagnosis and prognosis of the disease. Phosphoproteome is one of the most studied complements of the whole proteome given its importance in the understanding of cellular processes such as signaling and regulations. Over the last decade, several new methods have been developed for phosphoproteome analysis. A significant amount of these efforts pertains to cancer research. The current use of powerful analytical instruments in phosphoproteomic approaches has paved the way for deeper and sensitive investigations. However, these methods and techniques need further improvements to deal with challenges posed by the complexity of samples and scarcity of phosphoproteins in the whole proteome, throughput and reproducibility. This review aims to provide a comprehensive summary of the variety of steps used in phosphoproteomic methods applied in cancer research including the enrichment and fractionation strategies. This will allow researchers to evaluate and choose a better combination of steps for their phosphoproteome studies.
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Affiliation(s)
- Mustafa Gani Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Saime Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Syed Ghulam Musharraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Nesrin Emekli
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
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7
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Wang B, Wu H, Yan Y, Tang K, Ding CF. In situ synthesis of a novel metal oxide affinity chromatography affinity probe for the selective enrichment of low-abundance phosphopeptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8881. [PMID: 32638431 DOI: 10.1002/rcm.8881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/02/2020] [Accepted: 07/05/2020] [Indexed: 05/20/2023]
Abstract
RATIONALE Due to the dynamic nature of phosphorylation states and the low stoichiometry of phosphopeptides, it is still a challenge to efficiently capture phosphopeptides from complex biological samples before mass spectrometry analysis. Among the enrichment strategies, metal oxide affinity chromatography (MOAC) is one of the most widely used and the one with the most potential. It is based on reversible Lewis acid-base interactions between the metal oxides and the negatively charged phosphate groups to achieve the specific selection of phosphopeptides. METHODS A novel MOAC affinity probe, denoted as G@PDA@ZrO2 , was successfully synthesized by in situ grafting ZrO2 onto the surface of graphene (G) modified with polydopamine (PDA). The novel MOAC probe thus obtained was used for phosphopeptide enrichment. RESULTS This novel MOAC affinity probe when used to selectively enrich phosphopeptides from standard protein digest solutions exhibited a high selectivity (β-casein:bovine serum albumin = 1:1000), a low detection limit (4 fmol), and a high loading capacity (400 mg/g). At the same time, the experimental results proved that G@PDA@ZrO2 had great recyclability (five cycles), stability, and reproducibility. Subsequently, G@PDA@ZrO2 was applied to enrich phosphopeptides from human saliva and human serum, in which 25 and 4 phosphopeptide peaks, respectively, were detected. CONCLUSIONS This novel MOAC affinity probe (G@PDA@ZrO2 ) showed good performance in enriching phosphopeptides. Thus, G@PDA@ZrO2 has good potential in phosphopeptidomics analysis.
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Affiliation(s)
- Baichun Wang
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Huanming Wu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, China
| | - Yinghua Yan
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Keqi Tang
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Chuan-Fan Ding
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
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8
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Dual metal cations coated magnetic mesoporous silica probe for highly selective capture of endogenous phosphopeptides in biological samples. Mikrochim Acta 2020; 187:400. [DOI: 10.1007/s00604-020-04323-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/14/2020] [Indexed: 11/25/2022]
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9
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A new opening for the tricky untargeted investigation of natural and modified short peptides. Talanta 2020; 219:121262. [PMID: 32887153 DOI: 10.1016/j.talanta.2020.121262] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022]
Abstract
Short peptides are of extreme interest in clinical and food research fields, nevertheless they still represent a crucial analytical issue. The main aim of this paper was the development of an analytical platform for a considerable advancement in short peptides identification. For the first time, short sequences presenting both natural and post-translationally modified amino acids were comprehensively studied thanks to the generation of specific databases. Short peptide databases had a dual purpose. First, they were employed as inclusion lists for a suspect screening mass-spectrometric analysis, overcoming the limits of data dependent acquisition mode and allowing the fragmentation of such low-abundance substances. Moreover, the databases were implemented in Compound Discoverer 3.0, a software dedicated to the analysis of short molecules, for the creation of a data processing workflow specifically dedicated to short peptide tentative identification. For this purpose, a detailed study of short peptide fragmentation pathways was carried out for the first time. The proposed method was applied to the study of short peptide sequences in enriched urine samples and led to the tentative identification more than 200 short natural and modified short peptides, the highest number ever reported.
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10
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Capriotti AL, Cerrato A, Laganà A, Montone CM, Piovesana S, Zenezini Chiozzi R, Cavaliere C. Development of a Sample-Preparation Workflow for Sulfopeptide Enrichment: From Target Analysis to Challenges in Shotgun Sulfoproteomics. Anal Chem 2020; 92:7964-7971. [DOI: 10.1021/acs.analchem.0c01342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, Netherlands
- Netherlands Proteomics CentrePadualaan 8Utrecht3584 CHNetherlands
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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11
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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12
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Peng J, Zhang H, Niu H, Wu R. Peptidomic analyses: The progress in enrichment and identification of endogenous peptides. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115835] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Capriotti AL, Antonelli M, Antonioli D, Cavaliere C, Chiarcos R, Gianotti V, Piovesana S, Sparnacci K, Laus M, Laganà A. Effect of shell structure of Ti-immobilized metal ion affinity chromatography core-shell magnetic particles for phosphopeptide enrichment. Sci Rep 2019; 9:15782. [PMID: 31673007 PMCID: PMC6823385 DOI: 10.1038/s41598-019-51995-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022] Open
Abstract
Magnetic materials in sample preparation for shotgun phosphoproteomics offer several advantages over conventional systems, as the enrichment can be achieved directly in solution, but they still suffer from some drawbacks, due to limited stability and selectivity, which is supposed to be affected by the hydrophilicity of the polymeric supports used for cation immobilization. The paper describes the development of an improved magnetic material with increased stability, thanks to a two-step covering of the magnetic core, for the enrichment of phosphopeptides in biological samples. Four materials were prepared featuring a polymeric shell with tunable hydrophilicity, obtained by "grafting from" polymerization of glycidyl methacrylate with 0-8.3% of polyethylene glycol methacrylate (PEGMA), the latter used to modulate the hydrophilicity of the material surface. Finally, the materials were functionalized with iminodiacetic acid for Ti4+ ion immobilization. The materials were analyzed for their composition by a combination of CHN elemental analysis and thermogravimetric analysis, also hyphenated to gas chromatography and mass spectrometric detection. Surface characteristics were evaluated by water contact angle measurements, scanning electron microscopy and energy dispersive X-ray spectrometry. These materials were applied to the enrichment of phosphopeptides from yeast protein digests. Peptides were identified by proteomics techniques using nano-high performance liquid chromatography coupled to mass spectrometry and bioinformatics. Qualitatively the peptides identified by the four systems were comparable, with 1606-1693 phosphopeptide identifications and a selectivity of 47-54% for all materials. The physico-chemical features of the identified peptides were also the same for the four materials. In particular, the grand average of hydropathy index values indicated that the enriched phosphopeptides were hydrophilic (ca. 90%), and only some co-enriched non-phosphorylated peptides were hydrophobic (21-28%), regardless of the material used for enrichment. Peptides had a pI ≤ 7, which indicated a well-known bias for acidic peptides binding, attributed to the interaction with the metal center itself. The results indicated that the enrichment of phosphopeptides and the co-enrichment of non-phosphorylated peptides is mainly driven by interactions with Ti4+ and does not depend on the amount of PEGMA chains in the polymer shell.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Michela Antonelli
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Diego Antonioli
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Riccardo Chiarcos
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
| | - Valentina Gianotti
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Katia Sparnacci
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Michele Laus
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
- CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100, Lecce, Italy
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Seidi S, Tajik M, Baharfar M, Rezazadeh M. Micro solid-phase extraction (pipette tip and spin column) and thin film solid-phase microextraction: Miniaturized concepts for chromatographic analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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15
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Capriotti AL, Cavaliere C, La Barbera G, Montone CM, Piovesana S, Laganà A. Recent Applications of Magnetic Solid-phase Extraction for Sample Preparation. Chromatographia 2019. [DOI: 10.1007/s10337-019-03721-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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16
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Sensitive untargeted identification of short hydrophilic peptides by high performance liquid chromatography on porous graphitic carbon coupled to high resolution mass spectrometry. J Chromatogr A 2018; 1590:73-79. [PMID: 30611530 DOI: 10.1016/j.chroma.2018.12.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/14/2018] [Accepted: 12/30/2018] [Indexed: 12/20/2022]
Abstract
The combination of an efficient chromatographic separation with post-column addition of a supercharging agent was evaluated for the determination of small peptides. The procedure takes advantage of porous graphitic carbon (PGC) ability in retaining very polar and ionic molecules to overstep the poor retention of small peptides on conventional reversed phase (RP) columns. The method was developed specifically for the most hydrophilic di-, tri- and tetrapeptides, which are not identified in ordinary peptidomics experiments. In addition to retention mechanisms acting on conventional RP, the method exploited the charge induced interactions generated by the charges on the peptides with the polarizable surface of PGC. This results in efficient retention of very short and highly polar peptides using classical RP mobile phases. The effects of varying mobile phase composition (organic solvent and ion-pairing additives) as well as column temperature have been thoroughly investigated using short peptide standards. Under optimized conditions (water and acetonitrile/tetrahydrofuran 99:1 (v/v), both with 0.15% trifluoroacetic acid, as phase A and B, respectively, 0.5 mL min-1 flowrate at 50 °C) the effect of post-column addition of 3-nitrobenzylic alcohol was also investigated allowing effective coupling of the chromatographic system with high resolution mass spectrometry. Finally, an untargeted approach for peptide identification was pursued, based on precursor identification in database with all possible combinations of the 20 natural amino acids and fragmentation spectra matching to in silico generated spectra. The method was then applied to investigation of the short endogenous peptides in human serum from healthy individuals resulting in the identification of 30 short peptides.
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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Saliva as a source of new phosphopeptide biomarkers: Development of a comprehensive analytical method based on shotgun peptidomics. Talanta 2018; 183:245-249. [PMID: 29567172 DOI: 10.1016/j.talanta.2018.02.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022]
Abstract
The paper describes the development of an enrichment method for the analysis of the endogenous phosphopeptides in saliva. The method was based on magnetic solid phase extraction by a magnetic graphitized carbon black-TiO2 composite material and was developed considering different saliva pre-treatments, namely C18 solid phase extraction for purification, direct dilution in loading buffer or acetonitrile precipitation. The method was based on a shotgun proteomics workflow and the enriched peptide mixture was analysed by nanoHPLC and high resolution tandem mass spectrometry. Acetonitrile precipitation provided the best results, with up to 165 endogenous phosphopeptides identified in saliva samples from healthy individuals. The physico-chemical features of the identified endogenous phosphopeptides indicated that such peptides were large, hydrophilic and basic.
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