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Lv X, Jiao S, Wei Z, Cui C, Wang W, Tan Y, Pang G. Preparation of Core‐Shell Structured Magnetic Superhydrophilic Extractant for Enrichment of Phosphopeptides. ChemistrySelect 2022. [DOI: 10.1002/slct.202200821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xinyan Lv
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Shihui Jiao
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Zhonglin Wei
- Department of Organic Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Canyu Cui
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Wenwen Wang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Yumei Tan
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Guangsheng Pang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
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2
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Fe(III)-based immobilized metal-affinity chromatography (IMAC) method for the separation of the catechol siderophore from Bacillus tequilensis CD36. 3 Biotech 2018; 8:392. [PMID: 30175029 DOI: 10.1007/s13205-018-1396-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 08/07/2018] [Indexed: 12/15/2022] Open
Abstract
Catechol siderophore plays an important role in microbial ecology, agriculture, and medicine, but its research is often limited by the difficulty in acquisition of it in large quantities. Based on evidence from the coordination chemistry and chemical biology, catechol siderophore could chelate Fe3+ with high affinity. Therefore, Fe(III)-based immobilized metal-affinity chromatography (IMAC) was applied to capture siderophore from the culture filtrate of Bacillus tequilensis CD36. The ethanol-precipitated sample and the separated sample from Fe(III)-based IMAC were analyzed by liquid chromatography-mass spectrometry. According to the result, the pure siderophore DHB-Gly-Thr could be extracted from the ethanol-precipitated sample. Compared with other purifications, Fe(III)-based IMAC was convenient and had fewer steps. In addition, it also reduced the use of toxic chemical solvents in some traditional extraction process, such as extraction and ion exchange chromatography. Fe(III)-based IMAC was successfully used in separation of the catechol siderophore from B. tequilensis CD36. The results revealed that Fe(III)-based IMAC was an efficient and environmentally friendly method for the separation and purification of catechol siderophore.
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Araya-Farias M, Dziomba S, Carbonnier B, Guerrouache M, Ayed I, Aboud N, Taverna M, Tran NT. A lab-on-a-chip for monolith-based preconcentration and electrophoresis separation of phosphopeptides. Analyst 2017; 142:485-494. [DOI: 10.1039/c6an02324j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A real μTAS integrating monolith-based IMAC enrichment, electrophoresis separation and fluorescence detection of phosphopeptides is reported for the first time.
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Affiliation(s)
- Monica Araya-Farias
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - Szymon Dziomba
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | | | | | - Ichraf Ayed
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - Nacera Aboud
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - Myriam Taverna
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - N. Thuy Tran
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
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Affinity selection of histidine-containing peptides using metal chelate methacrylate monolithic disk for targeted LC–MS/MS approach in high-throughput proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 955-956:42-9. [DOI: 10.1016/j.jchromb.2014.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/08/2014] [Accepted: 02/12/2014] [Indexed: 11/18/2022]
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5
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Wang ZG, Cheng G, Liu YL, Zhang JL, Sun DH, Ni JZ. Novel core-shell cerium(IV)-immobilized magnetic polymeric microspheres for selective enrichment and rapid separation of phosphopeptides. J Colloid Interface Sci 2013; 417:217-26. [PMID: 24407680 DOI: 10.1016/j.jcis.2013.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/05/2013] [Accepted: 11/07/2013] [Indexed: 01/31/2023]
Abstract
In this work, novel magnetic polymeric core-shell structured microspheres with immobilized Ce(IV), Fe3O4@SiO2@PVPA-Ce(IV), were designed rationally and synthesized successfully via a facile route for the first time. Magnetic Fe3O4@SiO2 microspheres were first prepared by directly coating a thin layer of silica onto Fe3O4 magnetic particles using a sol-gel method, a poly(vinylphosphonic acid) (PVPA) shell was then coated on the Fe3O4@SiO2 microspheres to form Fe3O4@SiO2@PVPA microspheres through a radical polymerization reaction, and finally Ce(IV) ions were robustly immobilized onto the Fe3O4@SiO2@PVPA microspheres through strong chelation between Ce(IV) ions and phosphate moieties in the PVPA. The applicability of the Fe3O4@SiO2@PVPA-Ce(IV) microspheres for selective enrichment and rapid separation of phosphopeptides from proteolytic digests of standard and real protein samples was investigated. The results demonstrated that the core-shell structured Fe3O4@SiO2@PVPA-Ce(IV) microspheres with abundant Ce(IV) affinity sites and excellent magnetic responsiveness can effectively purify phosphopeptides from complex biosamples for MS detection taking advantage of the rapid magnetic separation and the selective affinity between Ce(IV) ions and phosphate moieties of the phosphopeptides. Furthermore, they can be effectively recycled and show good reusability, and have better performance than commercial TiO2 beads and homemade Fe3O4@PMAA-Ce(IV) microspheres. Thus the Fe3O4@SiO2@PVPA-Ce(IV) microspheres can benefit greatly the mass spectrometric qualitative analysis of phosphopeptides in phosphoproteome research.
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Affiliation(s)
- Zhi-Gang Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gong Cheng
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Lin Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Lin Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China.
| | - De-Hui Sun
- Changchun Institute Technology, Changchun 130012, China
| | - Jia-Zuan Ni
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun 130022, China; College of Life Science, Shenzhen University, Shenzhen 518060, China
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6
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Zhou H, Ye M, Dong J, Corradini E, Cristobal A, Heck AJR, Zou H, Mohammed S. Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium (IV) ion affinity chromatography. Nat Protoc 2013; 8:461-80. [PMID: 23391890 DOI: 10.1038/nprot.2013.010] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mass spectrometry (MS)-based proteomics has become the preferred tool for the analysis of protein phosphorylation. To be successful at such an endeavor, there is a requirement for an efficient enrichment of phosphopeptides. This is necessary because of the substoichiometric nature of phosphorylation at a given site and the complexity of the cell. Recently, new alternative materials have emerged that allow excellent and robust enrichment of phosphopeptides. These monodisperse microsphere-based immobilized metal ion affinity chromatography (IMAC) resins incorporate a flexible linker terminated with phosphonate groups that chelate either zirconium or titanium ions. The chelated zirconium or titanium ions bind specifically to phosphopeptides, with an affinity that is similar to that of other widely used metal oxide affinity chromatography materials (typically TiO(2)). Here we present a detailed protocol for the preparation of monodisperse microsphere-based Ti(4+)-IMAC adsorbents and the subsequent enrichment process. Furthermore, we discuss general pitfalls and crucial steps in the preparation of phosphoproteomics samples before enrichment and, just as importantly, in the subsequent mass spectrometric analysis. Key points such as lysis, preparation of the chromatographic system for analysis and the most appropriate methods for sequencing phosphopeptides are discussed. Bioinformatics analysis specifically relating to site localization is also addressed. Finally, we demonstrate how the protocols provided are appropriate for both single-protein analysis and the screening of entire phosphoproteomes. It takes ∼2 weeks to complete the protocol: 1 week to prepare the Ti(4+)-IMAC material, 2 d for sample preparation, 3 d for MS analysis of the enriched sample and 2 d for data analysis.
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Affiliation(s)
- Houjiang Zhou
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Celikbiçak O, Kaynar G, Atakay M, Güler U, Kayili HM, Salih B. Specific enrichment and direct detection of phosphopeptides on insoluble transition metal oxide particles in matrix-assisted laser desorption/ionization mass spectrometry applications. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:151-162. [PMID: 24308196 DOI: 10.1255/ejms.1228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Several transition metal oxides, such as iron (III), nickel (II) and zirconium (IV) oxides, were examined in detail for the specific enrichment and the purification of phosphopeptides from a digested peptide mixture solution. Phosphopeptide enrichment was performed on the metal oxide particles using a peptide mixture obtained bytryptic digestion of beta-casein. The mixture of protein digests containing bovine serum albumin (BSA): beta-casein digests (100:1 mole ratio) was also used for the phosphopeptide enrichment. Furthermore, non-fat milk digest was examined as a complex biological sample. In each phosphopeptide enrichment process, phosphopeptides were specifically enriched and separated from the non-phosphopeptides. The phosphopeptides were adsorbed onto the metal oxide surface at acidic pH values between 1.0 and 2.0 and, for desorption of phosphopeptides from metal oxide particles, pH values were examined and optimized in the enrichment studies. The analysis of phosphopeptides were carried out by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using 2,5-dihydroxybenzoic acid matrix containing 1.0% phosphoric acid to obtain intense protonated signals and to overcome degradation of the phosphopeptides by phosphate group loss in mass spectrometric conditions. Moreover, it was demonstrated that the direct detection of phosphopeptides from the surface of the metal oxide particles was possible using MALDI-MS by mixing the phosphopeptide-adsorbed metal oxide particles with MALDI matrix solution in slurry form before the analysis. Thus, the effects of interferences arising from chemical species used in the desorption process was successfully eliminated for the fast and sensitive detection of phosphopeptides in MALDI-MS applications.
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Affiliation(s)
- Omür Celikbiçak
- Hacettepe University, Department of Chemistry, 06800 Ankara, Turkey
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8
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Beltran L, Cutillas PR. Advances in phosphopeptide enrichment techniques for phosphoproteomics. Amino Acids 2012; 43:1009-24. [PMID: 22821267 DOI: 10.1007/s00726-012-1288-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 04/03/2012] [Indexed: 12/27/2022]
Abstract
Phosphoproteomics is increasingly used to address a wide range of biological questions. However, despite some success, techniques for phosphoproteomics are not without challenges. Phosphoproteins are present in cells in low abundance relative to their unphosphorylated counterparts; therefore phosphorylated proteins (or phosphopeptides after protein digestion) are rarely detected in standard shotgun proteomics experiments. Thus, extraction of phosphorylated polypeptides from complex mixtures is a critical step in the success of phosphoproteomics experiments. Intense research over the last decade has resulted in the development of powerful techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Here, we review how the development of IMAC, MOAC, chemical derivatization and antibody affinity purification and chromatography is contributing to the evolution of phosphoproteomics techniques. Although further developments are needed for the technology to reach maturity, current state-of-the-art techniques can already be used as powerful tools for biological research.
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Affiliation(s)
- Luisa Beltran
- Analytical Signalling Group, Centre for Cell Signalling, Barts Cancer Institute-CR-UK Centre of Excellence, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
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9
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Dong M, Ye M, Cheng K, Song C, Pan Y, Wang C, Bian Y, Zou H. Depletion of Acidic Phosphopeptides by SAX To Improve the Coverage for the Detection of Basophilic Kinase Substrates. J Proteome Res 2012; 11:4673-81. [DOI: 10.1021/pr300503z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mingming Dong
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kai Cheng
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunxia Song
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanbo Pan
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunli Wang
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- CAS Key Lab
of Separation Sciences
for Analytical Chemistry, National Chromatographic Research and Analysis
Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Liu H, Bao XL, Lv Y, Xu JT, Guo ST. Separation and Evaluation of Soybean Protein Hydrolysates Prepared by Immobilized Metal Ion Affinity Chromatography with Different Metal Ions. J Chromatogr Sci 2012; 50:714-20. [DOI: 10.1093/chromsci/bms071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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11
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Li X, Guo Z, Sheng Q, Xue X, Liang X. Sequential elution of multiply and singly phosphorylated peptides with polar-copolymerized mixed-mode RP18/SCX material. Analyst 2012; 137:2774-6. [DOI: 10.1039/c2an35247h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Chesnik M, Halligan B, Olivier M, Mirza SP. Sequential abundant ion fragmentation analysis (SAIFA): an alternative approach for phosphopeptide identification using an ion trap mass spectrometer. Anal Biochem 2011; 418:197-203. [PMID: 21855524 PMCID: PMC3188319 DOI: 10.1016/j.ab.2011.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 10/17/2022]
Abstract
Phosphorylation has been the most studied of all the posttranslational modifications of proteins. Mass spectrometry has emerged as a powerful tool for phosphomapping on proteins/peptides. Collision-induced dissociation (CID) of phosphopeptides leads to the loss of phosphoric or metaphosphoric acid as a neutral molecule, giving an intense neutral loss product ion in the mass spectrum. Dissociation of the neutral loss product ion identifies peptide sequence. This method of data-dependent constant neutral loss (DDNL) scanning analysis has been commonly used for mapping phosphopeptides. However, preferential losses of groups other than phosphate are frequently observed during CID of phosphopeptides. Ions that result from such losses are not identified during DDNL analysis due to predetermined scanning for phosphate loss. In this study, we describe an alternative approach for improved identification of phosphopeptides by sequential abundant ion fragmentation analysis (SAIFA). In this approach, there is no predetermined neutral loss molecule, thereby undergoing sequential fragmentation of abundant peak, irrespective of the moiety lost during CID. In addition to improved phosphomapping, the method increases the sequence coverage of the proteins identified, thereby increasing the confidence of protein identification. To the best of our knowledge, this is the first report to use SAIFA for phosphopeptide identification.
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Affiliation(s)
- Marla Chesnik
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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13
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Fíla J, Honys D. Enrichment techniques employed in phosphoproteomics. Amino Acids 2011; 43:1025-47. [PMID: 22002794 PMCID: PMC3418503 DOI: 10.1007/s00726-011-1111-z] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 09/26/2011] [Indexed: 11/28/2022]
Abstract
Rapid changes of protein phosphorylation play a crucial role in the regulation of many cellular processes. Being post-translationally modified, phosphoproteins are often present in quite low abundance and tend to co-exist with their unphosphorylated isoform within the cell. To make their identification more practicable, the use of enrichment protocols is often required. The enrichment strategies can be performed either at the level of phosphoproteins or at the level of phosphopeptides. Both approaches have their advantages and disadvantages. Most enriching strategies are based on chemical modifications, affinity chromatography to capture peptides and proteins containing negatively charged phosphate groups onto a positively charged matrix, or immunoprecipitation by phospho-specific antibodies. In this article, the most up-to-date enrichment techniques are discussed, taking into account their optimization, and highlighting their advantages and disadvantages. Moreover, these methods are compared to each other, revealing their complementary nature in providing comprehensive coverage of the phosphoproteome.
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Affiliation(s)
- Jan Fíla
- Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, Czech Republic
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Montoya A, Beltran L, Casado P, Rodríguez-Prados JC, Cutillas PR. Characterization of a TiO₂ enrichment method for label-free quantitative phosphoproteomics. Methods 2011; 54:370-8. [PMID: 21316455 PMCID: PMC3158853 DOI: 10.1016/j.ymeth.2011.02.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 12/05/2022] Open
Abstract
Phosphorylation is a protein post-translational modification with key roles in the regulation of cell biochemistry and signaling. In-depth analysis of phosphorylation using mass spectrometry is permitting the investigation of processes controlled by phosphorylation at the system level. A critical step of these phosphoproteomics methods involves the isolation of phosphorylated peptides from the more abundant unmodified peptides produced by the digestion of cell lysates. Although different techniques to enrich for phosphopeptides have been reported, there are limited data on their suitability for direct quantitative analysis by MS. Here we report a TiO(2) based enrichment method compatible with large-scale and label-free quantitative analysis by LC-MS/MS. Starting with just 500 μg of protein, the technique reproducibly isolated hundreds of peptides, >85% of which were phosphorylated. These results were obtained by using relatively short LC-MS/MS gradient runs (45 min) and without any previous separation step. In order to characterize the performance of the method for quantitative analyses, we employed label-free LC-MS/MS using extracted ion chromatograms as the quantitative readout. After normalization, phosphopeptides were quantified with good precision (coefficient of variation was 20% on average, n=900 phosphopeptides), linearity (correlation coefficients >0.98) and accuracy (deviations <20%). Thus, phosphopeptide ion signals correlated with the concentration of the respective phosphopeptide in samples, making the approach suitable for in-depth relative quantification of phosphorylation by label-free LC-MS/MS.
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Key Words
- acc, accuracy
- acn, acetonitrile
- amac, ammonium acetate
- cv, coefficient of variation
- imac, immobilized metal affinity chromatography
- lc–ms/ms, liquid chromatography tandem mass spectrometry
- ms, mass spectrometry
- scx, strong cation exchange
- tio2, titanium dioxide
- xic, extracted ion chromatogram
- biomarker
- cell signalling
- kinase
- label-free
- lc-ms/ms
- mass spectrometry
- phosphorylation
- phosphoproteomics
- quantitative analysis
- systems biology
- titanium dioxide
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Affiliation(s)
| | | | | | | | - Pedro R. Cutillas
- Analytical Signalling Laboratory, Centre for Cell Signalling, Barts Cancer Institute, Bart’s and the London School of Medicine, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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15
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Zhou H, Low TY, Hennrich ML, van der Toorn H, Schwend T, Zou H, Mohammed S, Heck AJR. Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Mol Cell Proteomics 2011; 10:M110.006452. [PMID: 21715320 DOI: 10.1074/mcp.m110.006452] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Metal and metal oxide chelating-based phosphopeptide enrichment technologies provide powerful tools for the in-depth profiling of phosphoproteomes. One weakness inherent to current enrichment strategies is poor binding of phosphopeptides containing multiple basic residues. The problem is exacerbated when strong cation exchange (SCX) is used for pre-fractionation, as under low pH SCX conditions phosphorylated peptides with multiple basic residues elute with the bulk of the tryptic digest and therefore require more stringent enrichment. Here, we report a systematic evaluation of the characteristics of a novel phosphopeptide enrichment approach based on a combination of low pH SCX and Ti(4+)-immobilized metal ion affinity chromatography (IMAC) comparing it one-to-one with the well established low pH SCX-TiO(2) enrichment method. We also examined the effect of 1,1,1,3,3,3-hexafluoroisopropanol (HFP), trifluoroacetic acid (TFA), or 2,5-dihydroxybenzoic acid (DHB) in the loading buffer, as it has been hypothesized that high levels of TFA and the perfluorinated solvent HFP improve the enrichment of phosphopeptides containing multiple basic residues. We found that Ti(4+)-IMAC in combination with TFA in the loading buffer, outperformed all other methods tested, enabling the identification of around 5000 unique phosphopeptides containing multiple basic residues from 400 μg of a HeLa cell lysate digest. In comparison, ∼ 2000 unique phosphopeptides could be identified by Ti(4+)-IMAC with HFP and close to 3000 by TiO(2). We confirmed, by motif analysis, the basic phosphopeptides enrich the number of putative basophilic kinases substrates. In addition, we performed an experiment using the SCX/Ti(4+)-IMAC methodology alongside the use of collision-induced dissociation (CID), higher energy collision induced dissociation (HCD) and electron transfer dissociation with supplementary activation (ETD) on considerably more complex sample, consisting of a total of 400 μg of triple dimethyl labeled MCF-7 digest. This analysis led to the identification of over 9,000 unique phosphorylation sites. The use of three peptide activation methods confirmed that ETD is best capable of sequencing multiply charged peptides. Collectively, our data show that the combination of SCX and Ti(4+)-IMAC is particularly advantageous for phosphopeptides with multiple basic residues.
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Affiliation(s)
- Houjiang Zhou
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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Rosenqvist H, Ye J, Jensen ON. Analytical strategies in mass spectrometry-based phosphoproteomics. Methods Mol Biol 2011; 753:183-213. [PMID: 21604124 DOI: 10.1007/978-1-61779-148-2_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phosphoproteomics, the systematic study of protein phosphorylation events and cell signaling networks in cells and tissues, is a rapidly evolving branch of functional proteomics. Current phosphoproteomics research provides a large toolbox of strategies and protocols that may assist researchers to reveal key regulatory events and phosphorylation-mediated processes in the cell and in whole organisms. We present an overview of sensitive and robust analytical methods for phosphopeptide analysis, including calcium phosphate precipitation and affinity enrichment methods such as IMAC and TiO(2). We then discuss various tandem mass spectrometry approaches for phosphopeptide sequencing and quantification, and we consider aspects of phosphoproteome data analysis and interpretation. Efficient integration of these stages of phosphoproteome analysis is highly important to ensure a successful outcome of large-scale experiments for studies of phosphorylation-mediated protein regulation.
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Affiliation(s)
- Heidi Rosenqvist
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, Scotland, UK
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17
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Ye J, Zhang X, Young C, Zhao X, Hao Q, Cheng L, Jensen ON. Optimized IMAC−IMAC Protocol for Phosphopeptide Recovery from Complex Biological Samples. J Proteome Res 2010; 9:3561-73. [DOI: 10.1021/pr100075x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juanying Ye
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Xumin Zhang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Clifford Young
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Xiaolu Zhao
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Qin Hao
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Lei Cheng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ole Nørregaard Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Fowler GJ, Mishra G, Easton CD, McArthur SL. A ToF-SSIMS study of plasma polymer-based patterned metal affinity surfaces. POLYMER 2009. [DOI: 10.1016/j.polymer.2009.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zhou LH, Kang GY, Kim KP. A binary matrix for improved detection of phosphopeptides in matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2264-2272. [PMID: 19551845 DOI: 10.1002/rcm.4139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Application of matrix-assisted laser-desorption/ionization mass spectrometry (MALDI MS) to analysis and characterization of phosphopeptides in peptide mixtures may have a limitation, because of the lower ionizing efficiency of phosphopeptides than nonphosphorylated peptides in MALDI MS. In this work, a binary matrix that consists of two conventional matrices of 3-hydroxypicolinic acid (3-HPA) and alpha-cyano-4-hydroxycinnamic acid (CCA) was tested for phosphopeptide analysis. 3-HPA and CCA were found to be hot matrices, and 3-HPA not as good as CCA and 2,5-dihydroxybenzoic acid (DHB) for peptide analysis. However, the presence of 3-HPA in the CCA solution with a volume ratio of 1:1 could significantly enhance ion signals for phosphopeptides in both positive-ion and negative-ion detection modes compared with the use of pure CCA or DHB, the most common phosphopeptide matrices. Higher signal intensities of phosphopeptides could be obtained with lower laser power using the binary matrix. Neutral loss of the phosphate group (-80 Da) and phosphoric acid (-98 Da) from the phosphorylated-residue-containing peptide ions with the binary matrix was decreased compared with CCA alone. In addition, since the crystal shape prepared with the binary matrix was more homogeneous than that prepared with DHB, searching for 'sweet' spots can be avoided. The sensitivity to detect singly or doubly phosphorylated peptides in peptide mixtures was higher than that obtained with pure CCA and as good as that obtained using DHB. We also used the binary matrix to detect the in-solution tryptic digest of the crude casein extracted from commercially available low fat milk sample, and found six phosphopeptides to match the digestion products of casein, based on mass-to-charge values and LIFT TOF-TOF spectra.
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Affiliation(s)
- Li-Hua Zhou
- Department of Molecular Biotechnology, Konkuk University, Seoul 143-701, Korea
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Bi H, Qiao L, Busnel JM, Devaud V, Liu B, Girault HH. TiO2 Printed Aluminum Foil: Single-Use Film for a Laser Desorption/Ionization Target Plate. Anal Chem 2009; 81:1177-83. [DOI: 10.1021/ac8024448] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hongyan Bi
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Liang Qiao
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Jean-Marc Busnel
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Valerie Devaud
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Baohong Liu
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Hubert H. Girault
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
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21
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Affinity chromatography of phosphorylated proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2008. [PMID: 18826062 DOI: 10.1007/978-1-59745-582-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
This chapter covers the use of immobilized metal ion affinity chromatography (IMAC) for enrichment of phosphorylated proteins. Some requirements for successful enrichment of these types of proteins are discussed. An experimental protocol and a set of application data are included to enable the scientist to obtain high-yield results in a very short time with pre-packed phospho-specific metal ion affinity resin (PMAC).
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Smith JC, Figeys D. Recent developments in mass spectrometry-based quantitative phosphoproteomicsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2008; 86:137-48. [DOI: 10.1139/o08-007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Protein phosphorylation is a reversible post-translational modification that is involved in virtually all eukaryotic cellular processes and has been studied in great detail in recent years. Many developments in mass spectrometry (MS)-based proteomics have been successfully applied to study protein phosphorylation in highly complicated samples. Furthermore, the emergence of a variety of enrichment strategies has allowed some of the challenges associated with low phosphorylation stoichiometry and phosphopeptide copy number to be overcome. The dynamic nature of protein phosphorylation complicates its analysis; however, a number of methods have been developed to successfully quantitate phosphorylation changes in a variety of cellular systems. The following review details some of the most recent breakthroughs in the study of protein phosphorylation, or phosphoproteomics, using MS-based approaches. The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics.
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Affiliation(s)
- Jeffrey C. Smith
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Smith JC, Lambert JP, Elisma F, Figeys D. Proteomics in 2005/2006: developments, applications and challenges. Anal Chem 2007; 79:4325-43. [PMID: 17477510 DOI: 10.1021/ac070741j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jeffrey C Smith
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ontario, Canada K1H 8M5
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Pan C, Xu S, Zhou H, Fu Y, Ye M, Zou H. Recent developments in methods and technology for analysis of biological samples by MALDI-TOF-MS. Anal Bioanal Chem 2006; 387:193-204. [PMID: 17086385 DOI: 10.1007/s00216-006-0905-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 09/28/2006] [Accepted: 09/29/2006] [Indexed: 10/24/2022]
Abstract
Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) is widely used in a variety of fields because it has the characteristics of speed, ease of use, high sensitivity, and wide detectable mass range for obtaining molecular weights and for structural characterization of macromolecules. In this article we summarize recent developments in matrix additives, new matrices, and sample-pretreatment methods using off-probe or on-probe techniques or nanomaterials for MALDI-TOF-MS analysis of biological samples.
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Affiliation(s)
- Chensong Pan
- National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
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Molle V, Zanella-Cleon I, Robin JP, Mallejac S, Cozzone AJ, Becchi M. Characterization of the phosphorylation sites of Mycobacterium tuberculosis serine/threonine protein kinases, PknA, PknD, PknE, and PknH by mass spectrometry. Proteomics 2006; 6:3754-66. [PMID: 16739134 DOI: 10.1002/pmic.200500900] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In Mycobacterium tuberculosis (Mtb), regulatory phosphorylation of proteins at serine and/or threonine residues by serine/threonine protein kinases (STPKs) is an emerging theme connected with the involvement of these enzymes in virulence mechanisms. The identification of phosphorylation sites in proteins provides a powerful tool to study signal transduction pathways and to identify the corresponding interaction networks. Detection of phosphorylated proteins as well as assignment of the phosphorylated sites in STPKs is a major challenge in proteomics since some of these enzymes might be interesting therapeutical targets. Using different strategies to identify phosphorylated residues, we report, in the present work, MS studies of the entire intracellular regions of recombinant protein kinases PknA, PknD, PknE, and PknH from Mtb. The on-target dephosphorylation/MALDI-TOF for identification of phosphorylated peptides was used in combination with LC-ESI/MS/MS for localization of phosphorylation sites. By doing so, seven and nine phosphorylated serine and/or threonine residues were identified as phosphorylation sites in the recombinant intracellular regions of PknA and PknH, respectively. The same technique led also to the identification of seven phosphorylation sites in each of the two recombinant kinases, PknD and PknE.
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Affiliation(s)
- Virginie Molle
- Institute of Biology and Chemistry of Proteins, CNRS/University of Lyon, IFR128, 7 passage du Vercors, 69367 Lyon Cedex 07, France
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Abstract
Phosphoproteomics can be defined as the comprehensive study of protein phosphorylation by identification of the phosphoproteins, exact mapping of the phosphorylation sites, quantification of phosphorylation, and eventually, revealing their biological function. Its place in today's research is vitally important to address the most fundamental question - how the phosphorylation events control most, if not all, of the cellular processes in a given organism? Despite the immense importance of phosphorylation, the analysis of phosphoproteins on a proteome-wide scale remains a formidable challenge. Nevertheless, several technologies have been developed, mostly in yeast and mammals, to conduct a large-scale phosphoproteomic study. Some of these technologies have been successfully applied to plants with a few modifications, resulting in documentation of phosphoproteins, phosphorylation site mapping, identification of protein kinase substrates, etc. at the global level. In this review, we summarize in vitro and in vivo approaches for detection and analysis of phosphoproteins including protein kinases and we discuss the importance of phosphoproteomics in understanding plant biology. These approaches along with bioinformatics will help plant researchers to design and apply suitable phosphoproteomic strategies in helping to find answers to their biological questions.
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Affiliation(s)
- Birgit Kersten
- RZPD German Resource Center for Genome Research GmbH, Berlin, Germany
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Pan C, Ye M, Liu Y, Feng S, Jiang X, Han G, Zhu J, Zou H. Enrichment of Phosphopeptides by Fe3+-Immobilized Mesoporous Nanoparticles of MCM-41 for MALDI and Nano-LC−MS/MS Analysis. J Proteome Res 2006; 5:3114-24. [PMID: 17081063 DOI: 10.1021/pr0600125] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fe3+-immobilized mesoporous molecular sieves MCM-41 with particle size of ca. 600 nm and pore size of ca. 3 nm is synthesized and applied to selectively trap and separate phosphopeptides from tryptic digest of proteins. For the capture of phosphopeptides, typically 10 microL of tryptic digest solution was first diluted to 1 mL by solution of ACN/0.1% TFA (50:50, v/v) and incubated with 10 microL of 0.1% acetic acid dispersed Fe3+-immobilized MCM-41 for 1 h under vibration. Fe3+-immobilized MCM-41 with trapped phosphopeptides was separated by centrifugation. The deposition was first washed with a volume of 300 microL of solution containing 100 mM NaCl in ACN/0.1% TFA (50:50, v/v) and followed by a volume of 300 microL of solution of 0.1% acetic acid to remove nonspecifically bound peptides. The nanoparticles with trapped phosphopeptides are mixed with 2,5-dihydroxybenzoic acid (2,5-DHB) and deposited onto the target for analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). It was found that phosphopeptides from tryptic digest of alpha-casein and beta-casein are effectively and specifically trapped on Fe3+-immobilized MCM-41 with few peptides nonspecifically adsorbed. After the extraction by Fe3+-immobilized MCM-41, the suppression to the detection of phosphopeptides caused by abundant nonphosphopeptides from tryptic digest is effectively eliminated, and the detection of phosphopeptides by MALDI is greatly enhanced with the value of signal-to-noise (S/N) increased by more than an order of magnitude. It is demonstrated that the mechanism of the adsorption of phosphopeptides on Fe3+-immobilized MCM-41 is based on the interaction between the Fe3+ and the phosphate group. Finally, Fe3+-immobilized MCM-41 is applied to extract phosphopeptides from tryptic digest of the lysate of mouse liver for phosphoproteome analysis by nano-LC-MS/MS.
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Affiliation(s)
- Chensong Pan
- National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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