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Lau JKC, Hopkinson AC, Siu KWM. Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study. J Phys Chem B 2024; 128:504-514. [PMID: 38190618 DOI: 10.1021/acs.jpcb.3c06767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
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Liepold T, Klafki HW, Kumar S, Walter J, Wirths O, Wiltfang J, Jahn O. Matrix Development for the Detection of Phosphorylated Amyloid-β Peptides by MALDI-TOF-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:505-512. [PMID: 36706152 PMCID: PMC9983008 DOI: 10.1021/jasms.2c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/20/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Amyloid-β (Aβ) peptides, including post-translationally modified variants thereof, are believed to play a key role in the onset and progression of Alzheimer's disease. Suggested modified Aβ species with potential disease relevance include Aβ peptides phosphorylated at serine in position eight (pSer8-Aβ) or 26 (pSer26-Aβ). However, the published studies on those Aβ peptides essentially relied on antibody-based approaches. Thus, complementary analyses by mass spectrometry, as shown for other modified Aβ variants, will be necessary not only to unambiguously verify the existence of phosphorylated Aβ species in brain samples but also to reveal their exact identity as to phosphorylation sites and potential terminal truncations. With the aim of providing a novel tool for addressing this still-unresolved issue, we developed a customized matrix formulation, referred to as TOPAC, that allows for improved detection of synthetic phosphorylated Aβ species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. When TOPAC was compared with standard matrices, we observed higher signal intensities but minimal methionine oxidation and phosphate loss for intact pSer8-Aβ(1-40) and pSer26-Aβ(1-40). Similarly, TOPAC also improved the mass spectrometric detection and sequencing of the proteolytic cleavage products pSer8-Aβ(1-16) and pSer26-Aβ(17-28). We expect that TOPAC will facilitate future efforts to detect and characterize endogenous phosphorylated Aβ species in biological samples and that it may also find its use in phospho-proteomic approaches apart from applications in the Aβ field.
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Affiliation(s)
- Thomas Liepold
- Neuroproteomics
Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Goettingen, Germany
| | - Hans-Wolfgang Klafki
- Department
of Psychiatry and Psychotherapy, University Medical Center Goettingen, Georg-August-University, 37075 Goettingen, Germany
| | - Sathish Kumar
- Department
of Neurology, University of Bonn, 53127 Bonn, Germany
| | - Jochen Walter
- Department
of Neurology, University of Bonn, 53127 Bonn, Germany
| | - Oliver Wirths
- Department
of Psychiatry and Psychotherapy, University Medical Center Goettingen, Georg-August-University, 37075 Goettingen, Germany
| | - Jens Wiltfang
- Department
of Psychiatry and Psychotherapy, University Medical Center Goettingen, Georg-August-University, 37075 Goettingen, Germany
| | - Olaf Jahn
- Neuroproteomics
Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Goettingen, Germany
- Department
of Psychiatry and Psychotherapy, University Medical Center Goettingen, Georg-August-University, 37075 Goettingen, Germany
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Kuzin AA, Stupnikova GS, Strelnikova PA, Danichkina KV, Indeykina MI, Pekov SI, Popov IA. Quantitative Assessment of Serine-8 Phosphorylated β-Amyloid Using MALDI-TOF Mass Spectrometry. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238406. [PMID: 36500498 PMCID: PMC9740911 DOI: 10.3390/molecules27238406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The study of the molecular mechanisms of the pathogenesis of Alzheimer's disease (AD) is extremely important for identifying potential therapeutic targets as well as early markers. In this regard, the study of the role of post-translational modifications (PTMs) of β-amyloid (Aβ) peptides is of particular relevance. Serine-8 phosphorylated forms (pSer8-Aβ) have been shown to have an increased aggregation capacity and may reflect the severity of amyloidosis. Here, an approach for quantitative assessment of pSer8-Aβ based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is proposed. The relative fraction of pSer8-Aβ was estimated in the total Aβ-pool with a detection limit of 1 fmol for pSer8-Aβ (1-16) and an accuracy of 2% for measurements in the reflectron mode. The sensitivity of the developed method is suitable for determining the proportion of phosphorylated peptides in biological samples.
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Affiliation(s)
- Andrey A. Kuzin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | | | - Polina A. Strelnikova
- Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | | | - Maria I. Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - Stanislav I. Pekov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
- Siberian State Medical University, 634050 Tomsk, Russia
- Correspondence: (S.I.P.); (I.A.P.)
| | - Igor A. Popov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Siberian State Medical University, 634050 Tomsk, Russia
- Correspondence: (S.I.P.); (I.A.P.)
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4
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Identification, production and bioactivity of casein phosphopeptides – A review. Food Res Int 2022; 157:111360. [DOI: 10.1016/j.foodres.2022.111360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
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Karki S, Meher AK, Inutan ED, Pophristic M, Marshall DD, Rackers K, Trimpin S, McEwen CN. Development of a robotics platform for automated multi-ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35 Suppl 1:e8449. [PMID: 30950108 DOI: 10.1002/rcm.8449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/02/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Successful coupling of a multi-ionization automated platform with commercially available mass spectrometers provides improved coverage of compounds in complex mixtures through implementation of new and traditional ionization methods. The versatility of the automated platform is demonstrated through coupling with mass spectrometers from two different vendors. Standards and complex biological samples were acquired using electrospray ionization (ESI), solvent-assisted ionization (SAI) and matrix-assisted ionization (MAI). METHODS The MS™ prototype automated platform samples from 96- or 384-well plates as well as surfaces. The platform interfaces with Thermo Fisher Scientific mass spectrometers by replacement of the IonMax source, and on Waters mass spectrometers with additional minor source inlet modifications. The sample is transferred to the ionization region using a fused-silica or metal capillary which is cleaned between acquisitions using solvents. For ESI and SAI, typically 1 μL of sample solution is drawn into the capillary tube and for ESI slowly dispensed near the inlet of the mass spectrometer with voltage placed on the delivering syringe barrel to which the tubing is attached, while for SAI the sample delivery tubing inserts into the inlet without the need for high voltage. For MAI, typically, 0.2 μL of matrix solution is drawn into the syringe before drawing 0.1 μL of the sample solution and dispensing to dry before insertion into the inlet. RESULTS A comparison study of a mixture of angiotensin I, verapamil, crystal violet, and atrazine representative of peptides, drugs, dyes, and herbicides using SAI, MAI, and ESI shows large differences in ionization efficiency of the various components. Solutions of a mixture of erythromycin and azithromycin in wells of a 384-microtiter well plate were mass analyzed at the rate of ca 1 min per sample using MAI and ESI. In addition, we report the analysis of bacterial extracts using automated MAI and ESI methods. Finally, the ability to perform surface analysis with the automated platform is also demonstrated by directly analyzing dyes separated on a thin-layer chromatography (TLC) plate and compounds extracted from the surface of a beef liver tissue section. CONCLUSIONS The prototype multi-ionization automated platform offers solid matrix introduction used with MAI, as well as solution introduction using either ESI or SAI. The combination of ionization methods extends the types of compounds which are efficiently ionized and is especially valuable with complex mixtures as demonstrated for bacterial extracts. While coupling of the automated multi-ionization platform to Thermo and Waters mass spectrometers is demonstrated, it should be possible to interface it with most commercial mass spectrometers.
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Affiliation(s)
- Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | - Anil K Meher
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | - Milan Pophristic
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, USA
| | | | | | - Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
- Cardiovascular Research Institute, Wayne State University, Detroit, MI, USA
| | - Charles N McEwen
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, USA
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Commodore JJ, Cassady CJ. Electron transfer dissociation mass spectrometry of acidic phosphorylated peptides cationized with trivalent praseodymium. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1178-1188. [PMID: 30221809 PMCID: PMC6291000 DOI: 10.1002/jms.4291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
The lanthanide ion praseodymium, Pr(III), was employed to study metallated ion formation and electron transfer dissociation (ETD) of 27 biological and model highly acidic phosphopeptides. All phosphopeptides investigated form metallated ions by electrospray ionization (ESI) that can be studied by ETD to yield abundant sequence information. The ions formed are [M + Pr - H]2+ , [M + Pr]3+ , and [M + Pr + H]4+ . All biological phosphopeptides with a chain length of seven or more residues generate [M + Pr]3+ . For biological phosphopeptides, [M + Pr]3+ undergoes more backbone cleavage by ETD than [M + Pr - H]2+ and, in some cases, full sequence coverage occurs. Acidic model phosphorylated hexa-peptides and octa-peptides, composed of alanine residues and one phosphorylated residue, form exclusively [M + Pr - H]2+ by ESI. Limited sequence information is obtained by ETD of [M + Pr - H]2+ with only metallated product ions being generated. For two biological phosphopeptides, [M + Pr + H]4+ is observed and may be due to the presence of at least one residue with a highly basic side chain that facilitates the addition of an extra proton. For the model phosphopeptides, more sequence coverage occurs when the phosphorylated residue is in the middle of the sequence than at either the N- or C-terminus. ETD of the metallated precursor ions formed by ESI generates exclusively metallated and nonmetallated c- and z-ions for the biological phosphopeptides, while metallated c-ions, z-ions, and a few y-ions form for the model phosphopeptides. Most of the product ions contain the phosphorylated residue indicating that the metal ion binds predominantly at the deprotonated phosphate group. The results of this study indicate that ETD is a promising tool for sequencing highly acidic phosphorylated peptides by metal adduction with Pr (III) and, by extension, all nonradioactive lanthanide metal ions.
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Affiliation(s)
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama, USA
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7
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Fatkullina AF, Yanybin VM, Asfandiarov NL, Tuktarov AR, Khalilov LM. MALDI Mass Spectrometry of Fullero[C60]tetrahydropyridines. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418070105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Herrera Y, Contreras S, Hernández M, Álvarez L, Mora Y, Encarnación-Guevara S. Displacers improve the selectivity of phosphopeptide enrichment by metal oxide affinity chromatography. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2018; 74:200-207. [PMID: 29382487 DOI: 10.1016/j.bmhimx.2017.03.008] [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: 03/06/2017] [Accepted: 03/17/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND A key process in cell regulation is protein phosphorylation, which is catalyzed by protein kinases and phosphatases. However, phosphoproteomics studies are difficult because of the complexity of protein phosphorylation and the number of phosphorylation sites. METHODS We describe an efficient approach analyzing phosphopeptides in single, separated protein by two-dimensional gel electrophoresis. In this method, a titanium oxide (TiO2)-packed NuTip is used as a phosphopeptide trap, together with displacers as lactic acid in the loading buffer to increase the efficiency of the interaction between TiO2 and phosphorylated peptides. RESULTS The results were obtained from the comparison of mass spectra of proteolytic peptides of proteins with a matrix-assisted laser desorption-ionization-time of flight (MALDI-TOF) instrument. CONCLUSIONS This method has been applied to identifying phosphoproteins involved in the symbiosis Rhizobium etli-Phaseolus vulgaris.
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Affiliation(s)
- Yesenia Herrera
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Sandra Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Magdalena Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Laura Álvarez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Yolanda Mora
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Halim MA, MacAleese L, Lemoine J, Antoine R, Dugourd P, Girod M. Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:270-283. [PMID: 28980177 DOI: 10.1007/s13361-017-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Luke MacAleese
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| | - Rodolphe Antoine
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France.
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
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Hountondji C, Créchet JB, Le Caër JP, Lancelot V, Cognet JAH, Baouz S. Affinity labelling in situ of the bL12 protein on E. coli 70S ribosomes by means of a tRNA dialdehyde derivative. J Biochem 2017; 162:437-448. [DOI: 10.1093/jb/mvx055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/29/2017] [Indexed: 11/14/2022] Open
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Elnegaard RLB, Møllegaard NE, Zhang Q, Kjeldsen F, Jørgensen TJD. Uranyl Photocleavage of Phosphopeptides Yields Truncated C-Terminally Amidated Peptide Products. Chembiochem 2017; 18:1117-1122. [PMID: 28425166 PMCID: PMC5488209 DOI: 10.1002/cbic.201700103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Indexed: 12/24/2022]
Abstract
The uranyl ion (UO22+) binds phosphopeptides with high affinity, and when irradiated with UV‐light, it can cleave the peptide backbone. In this study, high‐accuracy tandem mass spectrometry and enzymatic assays were used to characterise the photocleavage products resulting from the uranyl photocleavage reaction of a tetraphosphorylated β‐casein model peptide. We show that the primary photocleavage products of the uranyl‐catalysed reaction are C‐terminally amidated. This could be of great interest to the pharmaceutical industry, as efficient peptide amidation reactions are one of the top challenges in green pharmaceutical chemistry.
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Affiliation(s)
- Rasmus L B Elnegaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Niels Erik Møllegaard
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Qiang Zhang
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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Chan CYX, Gritsenko MA, Smith RD, Qian WJ. The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. Expert Rev Proteomics 2016; 13:421-33. [PMID: 26960075 DOI: 10.1586/14789450.2016.1164604] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.
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Affiliation(s)
- Chi Yuet X'avia Chan
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Marina A Gritsenko
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Richard D Smith
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
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13
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Unification of [FeFe]-hydrogenases into three structural and functional groups. Biochim Biophys Acta Gen Subj 2016; 1860:1910-21. [DOI: 10.1016/j.bbagen.2016.05.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/22/2022]
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14
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Marshall DD, Inutan ED, Wang B, Liu CW, Thawoos S, Wager-Miller J, Mackie K, Trimpin S. A broad-based study on hyphenating new ionization technologies with MS/MS for PTMs and tissue characterization. Proteomics 2016; 16:1695-706. [DOI: 10.1002/pmic.201500530] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/27/2016] [Accepted: 04/11/2016] [Indexed: 01/06/2023]
Affiliation(s)
| | - Ellen D. Inutan
- Department of Chemistry; Wayne State University; Detroit MI USA
| | - Beixi Wang
- Department of Chemistry; Wayne State University; Detroit MI USA
| | - Chih-Wei Liu
- Department of Chemistry; Wayne State University; Detroit MI USA
| | | | - James Wager-Miller
- Department of Psychological & Brain Sciences; Indiana University; Bloomington IN USA
| | - Ken Mackie
- Department of Psychological & Brain Sciences; Indiana University; Bloomington IN USA
| | - Sarah Trimpin
- Department of Chemistry; Wayne State University; Detroit MI USA
- Cardiovascular Research Institute; Wayne State University School of Medicine; Detroit MI USA
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16
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Takahashi H, Sekiya S, Nishikaze T, Kodera K, Iwamoto S, Wada M, Tanaka K. Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry. Anal Chem 2016; 88:3810-6. [DOI: 10.1021/acs.analchem.5b04888] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hidenori Takahashi
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Sadanori Sekiya
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Takashi Nishikaze
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Kei Kodera
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Motoi Wada
- Graduate
School of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Koichi Tanaka
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
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17
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Stover ML, Plummer CE, Miller SR, Cassady CJ, Dixon DA. Gas-Phase Acidities of Phosphorylated Amino Acids. J Phys Chem B 2015; 119:14604-21. [DOI: 10.1021/acs.jpcb.5b08616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele L. Stover
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Chelsea E. Plummer
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Sean R. Miller
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Carolyn J. Cassady
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - David A. Dixon
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
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18
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Abstract
Protein phosphorylation is a ubiquitous posttranslational modification, which is heavily involved in signal transduction. Misregulation of protein phosphorylation is often associated with a decrease in cell viability and complex diseases such as cancer. The dynamic and low abundant nature of phosphorylated proteins makes studying phosphoproteome a challenging task. In this review, we summarize state of the art proteomic techniques to study and quantify peptide phosphorylation in biological systems and discuss their limitations. Due to its short-lived nature, the phosphorylation event cannot be precisely traced in a heterogonous cell population, which highlights the importance of analyzing phosphorylation events at the single cell level. Mainly, we focus on the methodical and instrumental developments in proteomics and nanotechnology, which will help to build more accurate and robust systems for the feasibility of phosphorylation analysis at the single cell level. We propose that an automated and miniaturized construction of analytical systems holds the key to the future of phosphoproteomics; therefore, we highlight the benchmark studies in this direction. Having advanced and automated microfluidic chip LC systems will allow us to analyze single-cell phosphoproteomics and quantitatively compare it with others. The progress in the microfluidic chip LC systems and feasibility of the single-cell phosphoproteomics will be beneficial for early diagnosis and detection of the treatment response of many crucial diseases.
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Affiliation(s)
- Ayse Nur Polat
- Department of Molecular Biology and Genetics, Science Faculty, Koç University, Istanbul, Turkey.
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19
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Shi C, Deng C. Immobilized metal ion affinity chromatography ZipTip pipette tip with polydopamine modification and Ti 4+ immobilization for selective enrichment and isolation of phosphopeptides. Talanta 2015; 143:464-468. [DOI: 10.1016/j.talanta.2015.05.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 12/22/2022]
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20
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Suni V, Imanishi SY, Maiolica A, Aebersold R, Corthals GL. Confident Site Localization Using a Simulated Phosphopeptide Spectral Library. J Proteome Res 2015; 14:2348-59. [DOI: 10.1021/acs.jproteome.5b00050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Veronika Suni
- Turku
Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
- Turku Centre for Computer Science, Joukahaisenkatu 3-5 B, FI-20520 Turku, Finland
| | - Susumu Y. Imanishi
- Turku
Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
| | - Alessio Maiolica
- Department
of Biology, Institute of Molecular Systems Biology, ETH Zurich, HPT E 51,
Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Department
of Biology, Institute of Molecular Systems Biology, ETH Zurich, HPT E 51,
Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
- Faculty
of Science, University of Zurich, 8057 Zurich, Switzerland
| | - Garry L. Corthals
- Turku
Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
- Van
’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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21
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Cui L, Yapici I, Borhan B, Reid GE. Quantification of competing H3PO4 versus HPO3 + H2O neutral losses from regioselective 18O-labeled phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:141-148. [PMID: 24249041 DOI: 10.1007/s13361-013-0744-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/26/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Abundant neutral losses of 98 Da are often observed upon ion trap CID-MS/MS of protonated phosphopeptide ions. Two competing fragmentation pathways are involved in this process, namely, the direct loss of H3PO4 from the phosphorylated residue and the combined losses of HPO3 and H2O from the phosphorylation site and from an additional site within the peptide, respectively. These competing pathways produce product ions with different structures but the same m/z values, potentially limiting the utility of CID-MS(3) for phosphorylation site localization. To quantify the relative contributions of these pathways and to determine the conditions under which each pathway predominates, we have examined the ion trap CID-MS/MS fragmentation of a series of regioselective (18)O-phosphate ester labeled phosphopeptides prepared using novel solution-phase amino acid synthesis and solid-phase peptide synthesis methodologies. By comparing the intensity of the -100 Da (-H3PO3 (18)O) versus -98 Da (-[HPO3 + H2O]) neutral loss product ions formed upon MS/MS, quantification of the two pathways was achieved. Factors that affect the extent of formation of the competing neutral losses were investigated, with the combined loss pathway predominantly occurring under conditions of limited proton mobility, and with increased combined losses observed for phosphothreonine compared with phosphoserine-containing peptides. The combined loss pathway was found to be less dominant under ion activation conditions associated with HCD-MS/MS. Finally, the contribution of carboxylic acid functional groups and backbone amide bonds to the water loss in the combined loss fragmentation pathway was determined via methyl esterification and by examination of a phosphopeptide lacking side-chain hydroxyl groups.
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Affiliation(s)
- Li Cui
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
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22
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Nika H, Nieves E, Hawke DH, Angeletti RH. Optimization of the β-elimination/michael addition chemistry on reversed-phase supports for mass spectrometry analysis of O-linked protein modifications. J Biomol Tech 2013; 24:132-53. [PMID: 23997661 PMCID: PMC3703673 DOI: 10.7171/jbt.13-2403-005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We previously adapted the β-elimination/Michael addition chemistry to solid-phase derivatization on reversed-phase supports, and demonstrated the utility of this reaction format to prepare phosphoseryl peptides in unfractionated protein digests for mass spectrometric identification and facile phosphorylation-site determination. Here, we have expanded the use of this technique to β-N-acetylglucosamine peptides, modified at serine/threonine, phosphothreonyl peptides, and phosphoseryl/phosphothreonyl peptides, followed in sequence by proline. The consecutive β-elimination with Michael addition was adapted to optimize the solid-phase reaction conditions for throughput and completeness of derivatization. The analyte remained intact during derivatization and was recovered efficiently from the silica-based, reversed-phase support with minimal sample loss. The general use of the solid-phase approach for enzymatic dephosphorylation was demonstrated with phosphoseryl and phosphothreonyl peptides and was used as an orthogonal method to confirm the identity of phosphopeptides in proteolytic mixtures. The solid-phase approach proved highly suitable to prepare substrates from low-level amounts of protein digests for phosphorylation-site determination by chemical-targeted proteolysis. The solid-phase protocol provides for a simple, robust, and efficient tool to prepare samples for phosphopeptide identification in MALDI mass maps of unfractionated protein digests, using standard equipment available in most biological laboratories. The use of a solid-phase analytical platform is expected to be readily expanded to prepare digest from O-glycosylated- and O-sulfonated proteins for mass spectrometry-based structural characterization.
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Affiliation(s)
- Heinz Nika
- Laboratory for Macromolecular Analysis and Proteomics and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; and
| | - Edward Nieves
- Laboratory for Macromolecular Analysis and Proteomics and
| | - David H. Hawke
- Department of Pathology, MD Anderson Cancer Center, University of Texas, Houston, Texas 77030, USA
| | - Ruth Hogue Angeletti
- Laboratory for Macromolecular Analysis and Proteomics and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; and
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23
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Zhang X, Wang F, Xia Y. Trypsin functionalization and zirconia coating of mesoporous silica nanotubes for matrix-assisted laser desorption/ionization mass spectrometry analysis of phosphoprotein. J Chromatogr A 2013; 1306:20-6. [DOI: 10.1016/j.chroma.2013.07.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/24/2013] [Accepted: 07/12/2013] [Indexed: 01/15/2023]
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24
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Engholm-Keller K, Larsen MR. Technologies and challenges in large-scale phosphoproteomics. Proteomics 2013; 13:910-31. [PMID: 23404676 DOI: 10.1002/pmic.201200484] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/18/2013] [Accepted: 01/31/2013] [Indexed: 12/23/2022]
Abstract
Phosphorylation, the reversible addition of a phosphate group to amino acid side chains of proteins, is a fundamental regulator of protein activity, stability, and molecular interactions. Most cellular processes, such as inter- and intracellular signaling, protein synthesis, degradation, and apoptosis, rely on phosphorylation. This PTM is thus involved in many diseases, rendering localization and assessment of extent of phosphorylation of major scientific interest. MS-based phosphoproteomics, which aims at describing all phosphorylation sites in a specific type of cell, tissue, or organism, has become the main technique for discovery and characterization of phosphoproteins in a nonhypothesis driven fashion. In this review, we describe methods for state-of-the-art MS-based analysis of protein phosphorylation as well as the strategies employed in large-scale phosphoproteomic experiments with focus on the various challenges and limitations this field currently faces.
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Affiliation(s)
- Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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25
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Schmidt A, Ammerer G, Mechtler K. Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho-site localization. Proteomics 2013; 13:945-54. [DOI: 10.1002/pmic.201200240] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/10/2012] [Accepted: 10/01/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Andreas Schmidt
- Christian-Doppler-Laboratory for Proteome Analysis; Department of Biochemistry and Microbiology; Max F. Perutz Laboratories; University of Vienna; Vienna Austria
- Institute for Molecular Pathology (IMP); Vienna Austria
| | - Gustav Ammerer
- Christian-Doppler-Laboratory for Proteome Analysis; Department of Biochemistry and Microbiology; Max F. Perutz Laboratories; University of Vienna; Vienna Austria
| | - Karl Mechtler
- Institute for Molecular Pathology (IMP); Vienna Austria
- Institute for Molecular Biotechnology of the Austrian Academy of Sciences (IMBA); Vienna Austria
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26
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Wetie AGN, Sokolowska I, Woods AG, Darie CC. Identification of Post-Translational Modifications by Mass Spectrometry. Aust J Chem 2013. [DOI: 10.1071/ch13144] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are the effector molecules of many cellular and biological processes and are thus very dynamic and flexible. Regulation of protein activity, structure, stability, and turnover is in part controlled by their post-translational modifications (PTMs). Common PTMs of proteins include phosphorylation, glycosylation, methylation, ubiquitination, acetylation, and oxidation. Understanding the biology of protein PTMs can help elucidate the mechanisms of many pathological conditions and provide opportunities for prevention, diagnostics, and treatment of these disorders. Prior to the era of proteomics, it was standard to use chemistry methods for the identification of protein modifications. With advancements in proteomic technologies, mass spectrometry has become the method of choice for the analysis of protein PTMs. In this brief review, we will highlight the biochemistry of PTMs with an emphasis on mass spectrometry.
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27
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Güzel Y, Rainer M, Mirza MR, Messner CB, Bonn GK. Highly selective recovery of phosphopeptides using trypsin-assisted digestion of precipitated lanthanide–phosphoprotein complexes. Analyst 2013; 138:2897-905. [DOI: 10.1039/c3an00066d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Cho K, Yoo JS, Kim EM, Kim JY, Kim YH, Oh HB, Yoo JS. A Multidimensional System for Phosphopeptide Analysis Using TiO2Enrichment and Ion-exchange Chromatography with Mass Spectrometry. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.10.3298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Abstract
Massive evidence suggests that genetic abnormalities contribute to the development of lung cancer. These molecular abnormalities may serve as diagnostic, prognostic and predictive biomarkers for this deadly disease. It is imperative to search these biomarkers in different tumorigenesis pathways so as to provide the most appropriate therapy for each individual patient with lung malignancy. Phosphoproteomics is a promising technology for the identification of biomarkers and novel therapeutic targets for cancer. Thousands of proteins interact via physical and chemical association. Moreover, some proteins can covalently modify other proteins post-translationally. These post-translational modifications ultimately give rise to the emergent functions of cells in sequence, space and time. Phosphoproteomics clinical researches imply the comprehensive analysis of the proteins that are expressed in cells or tissues and can be employed at different stages. In addition, understanding the functions of phosphorylated proteins requires the study of proteomes as linked systems rather than collections of individual protein molecules. In fact, proteomics approaches coupled with affinity chromatography strategies followed by mass spectrometry have been used to elucidate relevant biological questions. This article will discuss the relevant clues of post-translational modifications, phosphorylated proteins, and useful proteomics approaches to identify molecular cancer signatures. The recent progress in phosphoproteomics research in lung cancer will be also discussed.
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Affiliation(s)
- Elena López
- Hospital Universitario Niño Jesús, Department of Oncohematology of Children, Madrid 28009, Spain; E-Mail:
| | - William C. S. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +852-295-854-41; Fax: +852-295-854-55
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30
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Asakawa D, Sakakura M, Takayama M. Matrix effect on in-source decay products of peptides in matrix-assisted laser desorption/ionization. Mass Spectrom (Tokyo) 2012; 1:A0002. [PMID: 24349903 DOI: 10.5702/massspectrometry.a0002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/07/2012] [Indexed: 11/23/2022] Open
Abstract
MALDI-ISD of peptides were studied using several salicylic acid derivatives, 2,5-dihydroxybenzoic acid (2,5-DHB), 5-aminosalicylic acid (5-ASA), 5-formylsalicylic acid (5-FSA), and 5-nitrosalicylic acid (5-NSA) as matrices. The difference in the nature of the functional group at the 5-position in the salicylic acid derivatives can dramatically affect the ISD products. The use of 2,5-DHB and 5-ASA leads to "hydrogen-abundant" peptide radicals and subsequent radical-induced N-Cα bonds cleavage. N-Cα bond cleavage gave a c'/z (·) fragment pair and radical z (·)-series fragments gain a hydrogen radical or react with a matrix radical. In contrast, the use of 5-NSA resulted in the production of a "hydrogen-deficient" peptide radical that contained a radical site on the amide nitrogen in the peptide backbone. Subsequently, the radical site on the amide nitrogen induces Cα-C bond dissociation, leading to a (·)/x fragment pair. The a (·)-series ions undergo further hydrogen abstraction to form a-series ions after Cα-C bond cleavage. Since the Pro residue does not contain a nitrogen-centered radical site, Cα-C bond cleavage does not occur. Alternatively, the specific cleavage of CO-N bonds leads to a b (·)/y fragment pair at Xxx-Pro which occurs via hydrogen abstraction from the Cα-H in the Pro residue. The use of 5-FSA generated both a (·)/x- and c'/z (·)-series fragment pairs. An oxidizing matrix provides useful complementary information in MALDI-ISD compared to a reducing matrix for the analysis of amino acid sequencing and site localization in cases of phosphopeptides. MALDI-ISD, when used in conjunction with both reducing and oxidizing matrices is a potentially useful method for de novo peptide sequencing.
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Affiliation(s)
- Daiki Asakawa
- Mass Spectrometry Laboratory, Graduate School in Nanobioscience, Yokohama City University ; General and Physical Chemistry Department, Mass Spectrometry Laboratory, University of Liège
| | - Motoshi Sakakura
- Mass Spectrometry Laboratory, Graduate School in Nanobioscience, Yokohama City University
| | - Mitsuo Takayama
- Mass Spectrometry Laboratory, Graduate School in Nanobioscience, Yokohama City University
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31
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Nika H, Lee J, Willis IM, Angeletti RH, Hawke DH. Phosphopeptide characterization by mass spectrometry using reversed-phase supports for solid-phase β-elimination/Michael addition. J Biomol Tech 2012; 23:51-68. [PMID: 22951960 PMCID: PMC3324170 DOI: 10.7171/jbt.2012-2302-002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have adapted the Ba(2+) ion-catalyzed concurrent Michael addition reaction to solid-phase derivatization on ZipTip(C18) pipette tips using 2-aminoethanethiol as a nucleophile. This approach provides several advantages over the classical in-solution-based techniques, including ease of operation, completeness of reaction, improved throughput, efficient use of dilute samples, and amenability to automation. Phosphoseryl and phosphothreonyl peptides, as well as phosphoserine peptides with adjoining prolines, were used to optimize the reaction conditions, which proved highly compatible with the integrity of the samples. The analyte was recovered from the silica-based C18 resin at minimal sample loss. The use of the protocol for improved phosphopeptide detection by signal enhancement was demonstrated with low-level amounts of proteolytic digests from model proteins and experimental samples, an effect found especially prominent with multiple phosphorylated species. The reaction products proved highly suitable for structural characterization by collisionally induced dissociation (CID), and the resultant increased spectral information content, greatly facilitating mapping of the site of phosphorylation. In select cases, the method enables phosphorylation site localization within known protein sequences on the basis of single-stage data alone. The solid-phase strategy presented here provides a simple, versatile, and efficient tool for phosphopeptide structural characterization equipment readily available in most biological laboratories.
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Affiliation(s)
- Heinz Nika
- MD Anderson Cancer Center, The University of Texas, Houston, Texas 77030, USA; and
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | - Ruth Hogue Angeletti
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - David H. Hawke
- MD Anderson Cancer Center, The University of Texas, Houston, Texas 77030, USA; and
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32
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Lu Y, Zhou X, Stemmer PM, Reid GE. Sulfonium ion derivatization, isobaric stable isotope labeling and data dependent CID- and ETD-MS/MS for enhanced phosphopeptide quantitation, identification and phosphorylation site characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:577-93. [PMID: 21952753 PMCID: PMC4228788 DOI: 10.1007/s13361-011-0190-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/03/2011] [Accepted: 06/03/2011] [Indexed: 05/12/2023]
Abstract
An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded 'fixed charge' sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS(3), and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S'-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of 'light' (S(CH(3))(2)) and 'heavy' (S(CD(3))(2)) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS(3) or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency.
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Affiliation(s)
- Yali Lu
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
| | - Xiao Zhou
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Gavin E. Reid
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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33
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Asakawa D, Moriguchi S, Takayama M. Influence of amino acid composition and phosphorylation on the ion yields of peptides in MALDI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:108-115. [PMID: 22045543 DOI: 10.1007/s13361-011-0271-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 05/31/2023]
Abstract
The influence of arginine (Arg), lysine (Lys), and phenylalanine (Phe) residues and phosphorylation on the molecular ion yields of model peptides have been quantitatively studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry in both positive- and negative-ion mode. The results obtained from these experiments have been interpreted from the standpoint of two different components, namely, desorption and ionization, on the basis of the physicochemical properties of constituent amino acids of the model peptides. The presence of basic residues such as Arg and Lys enhanced the ion yields of protonated molecules [M + H](+). An N-terminal rather than a C-terminal Arg residue was advantageous for the formation of both [M + H](+) and [M - H](-). The presence of the Phe residue resulted in the increase of the ion yields of both [M + H](+) and [M - H](-). In contrast, the presence of phosphate group(s) contributed to the suppression of the yields of both [M + H](+) and [M - H](-) due to the loss of phosphate group. The detection limits for both [M + H](+) and [M - H](-) of model peptides have been evaluated.
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Affiliation(s)
- Daiki Asakawa
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Yokohama, 236-0027, Japan
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34
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Song H, Håkansson K. Electron detachment dissociation and negative ion infrared multiphoton dissociation of electrosprayed intact proteins. Anal Chem 2011; 84:871-6. [PMID: 22175525 DOI: 10.1021/ac202909z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In top-down proteomics, intact gaseous proteins are fragmented in a mass spectrometer by, e.g., electron capture dissociation (ECD) to obtain structural information. By far, most top-down approaches involve dissociation of protein cations. However, in electrospray ionization of phosphoproteins, the high acidity of phosphate may contribute to the formation of intramolecular hydrogen bonds or salt bridges, which influence subsequent fragmentation behavior. Other acidic proteins or proteins with regions containing multiple acidic residues may also be affected similarly. Negative ion mode, on the other hand, may enhance deprotonation and unfolding of multiply phosphorylated or highly acidic protein regions. Here, activated ion electron detachment dissociation (AI-EDD) and negative ion infrared multiphoton dissociation (IRMPD) were employed to investigate the fragmentation of intact proteins, including multiply phosphorylated β-casein, calmodulin, and glycosylated ribonuclease B. Compared to AI-ECD and positive ion IRMPD, AI-EDD and negative ion IRMPD provide complementary protein sequence information, particularly in regions with high acidity, including the multiply phosphorylated region of β-casein.
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35
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Tichy A, Salovska B, Rehulka P, Klimentova J, Vavrova J, Stulik J, Hernychova L. Phosphoproteomics: Searching for a needle in a haystack. J Proteomics 2011; 74:2786-97. [DOI: 10.1016/j.jprot.2011.07.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/13/2011] [Accepted: 07/22/2011] [Indexed: 11/27/2022]
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36
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Zhang Z. Prediction of Collision-Induced-Dissociation Spectra of Peptides with Post-translational or Process-Induced Modifications. Anal Chem 2011; 83:8642-51. [DOI: 10.1021/ac2020917] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhongqi Zhang
- Process and Product Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
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Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor. Proc Natl Acad Sci U S A 2011; 108:16212-6. [PMID: 21908710 DOI: 10.1073/pnas.1100012108] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The 14-3-3 family of phosphoserine/threonine-recognition proteins engage multiple nodes in signaling networks that control diverse physiological and pathophysiological functions and have emerged as promising therapeutic targets for such diseases as cancer and neurodegenerative disorders. Thus, small molecule modulators of 14-3-3 are much needed agents for chemical biology investigations and therapeutic development. To analyze 14-3-3 function and modulate its activity, we conducted a chemical screen and identified 4-[(2Z)-2-[4-formyl-6-methyl-5-oxo-3-(phosphonatooxymethyl)pyridin-2-ylidene]hydrazinyl]benzoate as a 14-3-3 inhibitor, which we termed FOBISIN (FOurteen-three-three BInding Small molecule INhibitor) 101. FOBISIN101 effectively blocked the binding of 14-3-3 with Raf-1 and proline-rich AKT substrate, 40 kD(a) and neutralized the ability of 14-3-3 to activate exoenzyme S ADP-ribosyltransferase. To provide a mechanistic basis for 14-3-3 inhibition, the crystal structure of 14-3-3ζ in complex with FOBISIN101 was solved. Unexpectedly, the double bond linking the pyridoxal-phosphate and benzoate moieties was reduced by X-rays to create a covalent linkage of the pyridoxal-phosphate moiety to lysine 120 in the binding groove of 14-3-3, leading to persistent 14-3-3 inactivation. We suggest that FOBISIN101-like molecules could be developed as an entirely unique class of 14-3-3 inhibitors, which may serve as radiation-triggered therapeutic agents for the treatment of 14-3-3-mediated diseases, such as cancer.
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Palumbo AM, Smith SA, Kalcic CL, Dantus M, Stemmer PM, Reid GE. Tandem mass spectrometry strategies for phosphoproteome analysis. MASS SPECTROMETRY REVIEWS 2011; 30:600-25. [PMID: 21294150 DOI: 10.1002/mas.20310] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.
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Affiliation(s)
- Amanda M Palumbo
- Department of Chemistry, Michigan State University, East Lansing, USA
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Trimpin S, Ren Y, Wang B, Lietz CB, Richards AL, Marshall DD, Inutan ED. Extending the Laserspray Ionization Concept to Produce Highly Charged Ions at High Vacuum on a Time-of-Flight Mass Analyzer. Anal Chem 2011; 83:5469-75. [DOI: 10.1021/ac2007976] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Yue Ren
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Beixi Wang
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Christopher B. Lietz
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Alicia L. Richards
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Darrell D. Marshall
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Ellen D. Inutan
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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Zhao PX, Zhao Y, Guo XF, Wang H, Zhang HS. Isolation of phosphopeptides using zirconium-chlorophosphonazo chelate-modified silica nanoparticles. J Chromatogr A 2011; 1218:2528-39. [DOI: 10.1016/j.chroma.2011.02.071] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 02/28/2011] [Accepted: 02/28/2011] [Indexed: 11/15/2022]
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Matheron L, Sachon E, Burlina F, Sagan S, Lequin O, Bolbach G. Sequence-Dependent Enrichment of a Model Phosphopeptide: A Combined MALDI-TOF and NMR Study. Anal Chem 2011; 83:3003-10. [DOI: 10.1021/ac103134e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucrèce Matheron
- Université P. et M. Curie Paris 6, UMR 7203 CNRS-UPMC-ENS, 4, Place Jussieu, 75005 Paris, Ecole Normale Supérieure, Département de Chimie, 24, rue Lhomond, 75005 Paris, France
- Plateforme de Spectrométrie de Masse et Protéomique, Université P. et M. Curie, IFR83, 7-9 Quai Saint Bernard, 75005 Paris, France
| | - Emmanuelle Sachon
- Université P. et M. Curie Paris 6, UMR 7203 CNRS-UPMC-ENS, 4, Place Jussieu, 75005 Paris, Ecole Normale Supérieure, Département de Chimie, 24, rue Lhomond, 75005 Paris, France
- Plateforme de Spectrométrie de Masse et Protéomique, Université P. et M. Curie, IFR83, 7-9 Quai Saint Bernard, 75005 Paris, France
| | - Fabienne Burlina
- Université P. et M. Curie Paris 6, UMR 7203 CNRS-UPMC-ENS, 4, Place Jussieu, 75005 Paris, Ecole Normale Supérieure, Département de Chimie, 24, rue Lhomond, 75005 Paris, France
| | - Sandrine Sagan
- Université P. et M. Curie Paris 6, UMR 7203 CNRS-UPMC-ENS, 4, Place Jussieu, 75005 Paris, Ecole Normale Supérieure, Département de Chimie, 24, rue Lhomond, 75005 Paris, France
| | - Olivier Lequin
- Université P. et M. Curie Paris 6, UMR 7203 CNRS-UPMC-ENS, 4, Place Jussieu, 75005 Paris, Ecole Normale Supérieure, Département de Chimie, 24, rue Lhomond, 75005 Paris, France
| | - Gérard Bolbach
- Université P. et M. Curie Paris 6, UMR 7203 CNRS-UPMC-ENS, 4, Place Jussieu, 75005 Paris, Ecole Normale Supérieure, Département de Chimie, 24, rue Lhomond, 75005 Paris, France
- Plateforme de Spectrométrie de Masse et Protéomique, Université P. et M. Curie, IFR83, 7-9 Quai Saint Bernard, 75005 Paris, France
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Zhou G, Yan X, Wu D, Kron SJ. Photocleavable peptide-conjugated magnetic beads for protein kinase assays by MALDI-TOF MS. Bioconjug Chem 2011; 21:1917-24. [PMID: 20860375 DOI: 10.1021/bc1003058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides were immobilized onto superparamagnetic beads via photocleavable linkers. This enabled simple, rapid, and label-free protein kinase assays via MALDI-TOF MS detection of substrate peptide phosphorylation. Abltide, a model substrate for the Abl protein tyrosine kinase model, was coupled onto amine-terminated beads, incubated with ATP and recombinant c-Abl kinase, and released and further detected to determine phosphorylation. Abltide phosphorylation was found to depend significantly on the length and composition of linkers to the bead surface. Inserting a diblock spacer of poly(glycine) and poly(ethylene glycol) segments markedly enhanced phosphorylation. To validate the assay, the activity of two small-molecule kinase inhibitors, imatinib and dasatinib, which target the oncogenic mutant tyrosine kinase Bcr-Abl to treat chronic myeloid leukemia (CML), was tested. Examining inhibition of the purified c-Abl or Bcr-Abl in K562 CML cell extracts, IC(50) values were determined to be consistent with the literature. This simple, label-free, MALDI-based protein kinase assay can be readily adapted to allow multiplexed assays of multiple peptide substrates and/or analysis of alternative post-translational modifications as a tool for drug discovery and clinical testing.
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Affiliation(s)
- Guangchang Zhou
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA
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Tyther R, McDonagh B, Sheehan D. Proteomics in investigation of protein nitration in kidney disease: technical challenges and perspectives from the spontaneously hypertensive rat. MASS SPECTROMETRY REVIEWS 2011; 30:121-141. [PMID: 21166007 DOI: 10.1002/mas.20270] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Kidneys are the mammalian organs with widest range of oxidative status ranging from the well-perfused cortex to the relatively anoxic medulla. This organ is of key interest from the perspective of hypertension, an important contributor to human mortality, and there has been growing use of the spontaneously hypertensive rat (SHR) as a model to explore oxidative stress in hypertensive kidney. Nitrosative stress is often associated with oxidative stress and, like oxidative stress, can lead to covalent modification of protein side-chains. It is especially relevant to kidney because of high levels of both nitrite/nitrate and nitric oxide synthase in medulla. Because of their relatively low abundance and their well-known role in signal transduction, nitration of tyrosines to 3-nitrotyrosines (3NT) is of particular interest in this regard. This modification has the potential to contribute to changes in regulation, in protein activity and may provide a means of specific targeting of key proteins. Mass spectrometry (MS) offers a promising route to detecting this modification. This review surveys protein nitration in kidney disease and highlights opportunities for MS detection of nitrated residues in the SHR.
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Affiliation(s)
- Raymond Tyther
- Upstream Bioprocessing Group, National Institute for Bioprocessing Research and Training, NICB, Dublin City University, Dublin, Ireland
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Eickner T, Mikkat S, Lorenz P, Sklorz M, Zimmermann R, Thiesen HJ, Glocker MO. EJMS protocol: systematic studies on TiO2-based phosphopeptide enrichment procedures upon in-solution and in-gel digestions of proteins. Are there readily applicable protocols suitable for matrix-assisted laser desorption/ionization mass spectrometry-based phosphopeptide stability estimations? EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2011; 17:507-523. [PMID: 22173543 DOI: 10.1255/ejms.1134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
There have been many successful efforts to enrich phosphopeptides in complex protein mixtures by the use of immobilized metal affinity chromatography (IMAC) and/or metal oxide affinity chromatography (MOAC) with which mass spectrometric analysis of phosphopeptides has become state of the art in specialized laboratories, mostly applying nanoLC electrospray ionization mass spectrometry-based investigations. However, widespread use of these powerful techniques is still not achieved. In this study, we present a ready-to-use phosphopeptide enrichment procedure using commercially available TiO(2)-loaded pipette tips in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analyses. Using α-casein as a model protein and citric acid as additive during sample loading, a similar enrichment success can be achieved as compared to applying 2,5- dihydroxy benzoic acid (DHB) for this task. But the DHB-inherited drawbacks are eliminated. In addition, we show that combining DHB and 2,4,6-trihydroxy acetophenone (THAP) as matrix for MALDI-MS measurements retains the sensitivity of DHB for phosphopeptide analysis but adds the homogenous crystallization properties of THAP, enabling preparation of evenly distributed matrix surfaces on MALDI-MS anchor targets, a prerequisite for automated MALDI- MS analyses. Tripartite motif-containing protein 28 and stathmin are two examples for which successful phosphopeptide enrichment of either sodium dodecyl sulfate polyacrylamide gel electrophoresis or two-dimensional gel electrophoresis-separated proteins is shown. Finally, high resolution MALDI Fourier transform ion cyclotron resonance mass spectrometry after phosphopeptide enrichment suggests that chemical dephosphorylation may occur as a side reaction during basic elution of phosphopeptides bound to MOAC surfaces, suggesting that proteome-wide phosphopeptide analyses ought to be interpreted with caution. In contrast, in-depth analysis of phosphopeptide/non-phosphorylated peptide siblings may be used to estimate stability differences of phosphorylation sites in individual proteins, possibly adding valuable information on biological regulation processes.
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Affiliation(s)
- Thomas Eickner
- Proteome Center Rostock, Medical Faculty, University of Rostock, Rostock, Germany
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Trost M, Bridon G, Desjardins M, Thibault P. Subcellular phosphoproteomics. MASS SPECTROMETRY REVIEWS 2010; 29:962-90. [PMID: 20931658 DOI: 10.1002/mas.20297] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Protein phosphorylation represents one of the most extensively studied post-translational modifications, primarily due to the emergence of sensitive methods enabling the detection of this modification both in vitro and in vivo. The availability of enrichment methods combined with sensitive mass spectrometry instrumentation has played a crucial role in uncovering the dynamic changes and the large expanding repertoire of this reversible modification. The structural changes imparted by the phosphorylation of specific residues afford exquisite mechanisms for the regulation of protein functions by modulating new binding sites on scaffold proteins or by abrogating protein-protein interactions. However, the dynamic interplay of protein phosphorylation is not occurring randomly within the cell but is rather finely orchestrated by specific kinases and phosphatases that are unevenly distributed across subcellular compartments. This spatial separation not only regulates protein phosphorylation but can also control the activity of other enzymes and the transfer of other post-translational modifications. While numerous large-scale phosphoproteomics studies highlighted the extent and diversity of phosphoproteins present in total cell lysates, the further understanding of their regulation and biological activities require a spatio-temporal resolution only achievable through subcellular fractionation. This review presents a first account of the emerging field of subcellular phosphoproteomics where cell fractionation approaches are combined with sensitive mass spectrometry methods to facilitate the identification of low abundance proteins and to unravel the intricate regulation of protein phosphorylation.
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Affiliation(s)
- Matthias Trost
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
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Pinto G, Caira S, Cuollo M, Lilla S, Fierro O, Addeo F. Hydroxyapatite as a concentrating probe for phosphoproteomic analyses. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:2669-78. [PMID: 20810326 DOI: 10.1016/j.jchromb.2010.07.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/27/2010] [Accepted: 07/27/2010] [Indexed: 11/17/2022]
Abstract
A novel method for the selective enrichment of casein phosphoproteins/phosphopeptides (CPP) from complex mixtures is reported herein. This method employs ceramic hydroxyapatite (HA) as a solid-phase adsorbent to efficiently capture phosphoproteins and CPP from complex media. Casein was chosen as the model phosphoprotein to test the protocol. CPP immobilized on HA microgranules formed a complex that was included in the matrix-assisted laser desorption/ionization mass spectrometry (MALDI) matrix before desorbing directly from the well plate. Casein fractions with different levels of phosphorylation were desorbed based upon the specific concentration of trifluoroacetic acid (TFA) included in the MALDI matrix. The HA-bound casein enzymolysis was performed in situ with trypsin to remove non-phosphorylated peptides and isolate the immobilized CPP. The latter were recovered by centrifugation, dried, and co-crystallized with a 1% phosphoric acid (PA) solution in the matrix that was appropriate for detecting CPP in MALDI-MS spectra. This approach for the selection of casein/CPP resulted in the identification of 32 CPP by MALDI-time of flight (TOF). The analytical process involved two steps requiring ∼2h, excluding the time required for the enzymatic reaction. The alkaline phosphatase (AP)-assisted de-phosphorylation of tryptic CPP allowed the phosphorylation level of peptides to be calculated concurrently with MALDI-TOF MS and liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS). The effectiveness of the extraction procedure assayed on eggshell phosphoproteins resulted in the identification of 5 phosphoproteins and 14 derived phosphopeptides with a phosphoprotein global recovery of ∼70% at least.
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Affiliation(s)
- Gabriella Pinto
- Department of Food Science, Faculty of Agriculture, University Federico II via Università 100, Parco Gussone, 80055 Portici, Italy.
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Eriksson A, Bergquist J, Edwards K, Hagfeldt A, Malmström D, Agmo Hernández V. Optimized Protocol for On-Target Phosphopeptide Enrichment Prior to Matrix-Assisted Laser Desorption−Ionization Mass Spectrometry Using Mesoporous Titanium Dioxide. Anal Chem 2010; 82:4577-83. [DOI: 10.1021/ac100589j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anna Eriksson
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Katarina Edwards
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Anders Hagfeldt
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - David Malmström
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Víctor Agmo Hernández
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden
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Enhanced MALDI-TOF MS analysis of phosphopeptides using an optimized DHAP/DAHC matrix. J Biomed Biotechnol 2010; 2010:759690. [PMID: 20339515 PMCID: PMC2842900 DOI: 10.1155/2010/759690] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/11/2009] [Accepted: 12/31/2009] [Indexed: 11/17/2022] Open
Abstract
Selecting an appropriate matrix solution is one of the most effective means of increasing the ionization efficiency of phosphopeptides in matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In this study, we systematically assessed matrix combinations of 2, 6-dihydroxyacetophenone (DHAP) and diammonium hydrogen citrate (DAHC), and demonstrated that the low ratio DHAP/DAHC matrix was more effective in enhancing the ionization of phosphopeptides. Low femtomole level of phosphopeptides from the tryptic digests of α-casein and β-casein was readily detected by MALDI-TOF-MS in both positive and negative ion mode without desalination or phosphopeptide enrichment. Compared with the DHB/PA matrix, the optimized DHAP/DAHC matrix yielded superior sample homogeneity and higher phosphopeptide measurement sensitivity, particularly when multiple phosphorylated peptides were assessed. Finally, the DHAP/DAHC matrix was applied to identify phosphorylation sites from α-casein and β-casein and to characterize two phosphorylation sites from the human histone H1 treated with Cyclin-Dependent Kinase-1 (CDK1) by MALDI-TOF/TOF MS.
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Picariello G, Ferranti P, Fierro O, Mamone G, Caira S, Di Luccia A, Monica S, Addeo F. Peptides surviving the simulated gastrointestinal digestion of milk proteins: Biological and toxicological implications. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:295-308. [DOI: 10.1016/j.jchromb.2009.11.033] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 11/10/2009] [Accepted: 11/17/2009] [Indexed: 11/27/2022]
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Gilley C, MacDonald M, Nachon F, Schopfer LM, Zhang J, Cashman JR, Lockridge O. Nerve agent analogues that produce authentic soman, sarin, tabun, and cyclohexyl methylphosphonate-modified human butyrylcholinesterase. Chem Res Toxicol 2010; 22:1680-8. [PMID: 19715348 DOI: 10.1021/tx900090m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The goal was to test 14 nerve agent model compounds of soman, sarin, tabun, and cyclohexyl methylphosphonofluoridate (GF) for their suitability as substitutes for true nerve agents. We wanted to know whether the model compounds would form the identical covalent adduct with human butyrylcholinesterase that is produced by reaction with true nerve agents. Nerve agent model compounds containing thiocholine or thiomethyl in place of fluorine or cyanide were synthesized as Sp and Rp stereoisomers. Purified human butyrylcholinesterase was treated with a 45-fold molar excess of nerve agent analogue at pH 7.4 for 17 h at 21 degrees C. The protein was denatured by boiling and was digested with trypsin. Aged and nonaged active site peptide adducts were quantified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry of the tryptic digest mixture. The active site peptides were isolated by HPLC and analyzed by MALDI-TOF-TOF mass spectrometry. Serine 198 of butyrylcholinesterase was covalently modified by all 14 compounds. Thiocholine was the leaving group in all compounds that had thiocholine in place of fluorine or cyanide. Thiomethyl was the leaving group in the GF thiomethyl compounds. However, sarin thiomethyl compounds released either thiomethyl or isopropyl, while soman thiomethyl compounds released either thiomethyl or pinacolyl. Thiocholine compounds reacted more rapidly with butyrylcholinesterase than thiomethyl compounds. Labeling with the model compounds resulted in aged adducts that had lost the O-alkyl group (O-ethyl for tabun, O-cyclohexyl for GF, isopropyl for sarin, and pinacolyl for soman) in addition to the thiocholine or thiomethyl group. The nerve agent model compounds containing thiocholine and the GF thiomethyl analogue were found to be suitable substitutes for true soman, sarin, tabun, and GF in terms of the adduct that they produced with human butyrylcholinesterase. However, the soman and sarin thiomethyl compounds yielded two types of adducts, one of which was thiomethyl phosphonate, a modification not found after treatment with authentic soman and sarin.
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Affiliation(s)
- Cynthia Gilley
- Human BioMolecular Research Institute, San Diego, California 92121, USA
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