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Lan T, Dong Y, Jiang L, Zhang Y, Sui X. Analytical approaches for assessing protein structure in protein-rich food: A comprehensive review. Food Chem X 2024; 22:101365. [PMID: 38623506 PMCID: PMC11016869 DOI: 10.1016/j.fochx.2024.101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
This review focuses on changes in nutrition and functional properties of protein-rich foods, primarily attributed to alterations in protein structures. We provide a comprehensive overview and comparison of commonly used laboratory methods for protein structure identification, aiming to offer readers a convenient understanding of these techniques. The review covers a range of detection technologies employed in food protein analysis and conducts an extensive comparison to identify the most suitable method for various proteins. While these techniques offer distinct advantages for protein structure determination, the inherent complexity of food matrices presents ongoing challenges. Further research is necessary to develop and enhance more robust detection methods to improve accuracy in protein conformation and structure analysis.
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Affiliation(s)
- Tian Lan
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yabo Dong
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lianzhou Jiang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaonan Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
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2
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Peker T, Zagiel B, Rocard L, Bich C, Sachon E, Moumné R. Analytical Tools for Dynamic Combinatorial Libraries of Cyclic Peptides. Chembiochem 2023; 24:e202300688. [PMID: 37815502 DOI: 10.1002/cbic.202300688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
Target-directed dynamic combinatorial chemistry is a very attractive strategy for the discovery of bioactive peptides. However, its application has not yet been demonstrated, presumably due to analytical challenges that arise from the diversity of a peptide library with combinatorial side-chains. We previously reported an efficient method to generate, under biocompatible conditions, large dynamic libraries of cyclic peptides grafted with amino acid's side-chains, by thiol-to-thioester exchanges. In this work, we present analytical tools to easily characterize such libraries by HPLC and mass spectrometry, and in particular to simplify the isomers' distinction requiring sequencing by MS/MS fragmentations. After structural optimization, the cyclic scaffold exhibits a UV-tag, absorbing at 415 nm, and an ornithine residue which favors the regioselective ring-opening and simultaneous MS/MS fragmentation, in the gas-phase.
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Affiliation(s)
- Taleen Peker
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Benjamin Zagiel
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Lou Rocard
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Emmanuelle Sachon
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- MS3U Platform, Fédération de Chimie Moléculaire de Paris Centre - FR2769, Sorbonne Université, 4 Place Jussieu, 75005, Paris, France
| | - Roba Moumné
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
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3
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Song JG, Baral KC, Kim GL, Park JW, Seo SH, Kim DH, Jung DH, Ifekpolugo NL, Han HK. Quantitative analysis of therapeutic proteins in biological fluids: recent advancement in analytical techniques. Drug Deliv 2023; 30:2183816. [PMID: 36880122 PMCID: PMC10003146 DOI: 10.1080/10717544.2023.2183816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Pharmaceutical application of therapeutic proteins has been continuously expanded for the treatment of various diseases. Efficient and reliable bioanalytical methods are essential to expedite the identification and successful clinical development of therapeutic proteins. In particular, selective quantitative assays in a high-throughput format are critical for the pharmacokinetic and pharmacodynamic evaluation of protein drugs and to meet the regulatory requirements for new drug approval. However, the inherent complexity of proteins and many interfering substances presented in biological matrices have a great impact on the specificity, sensitivity, accuracy, and robustness of analytical assays, thereby hindering the quantification of proteins. To overcome these issues, various protein assays and sample preparation methods are currently available in a medium- or high-throughput format. While there is no standard or universal approach suitable for all circumstances, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay often becomes a method of choice for the identification and quantitative analysis of therapeutic proteins in complex biological samples, owing to its high sensitivity, specificity, and throughput. Accordingly, its application as an essential analytical tool is continuously expanded in pharmaceutical R&D processes. Proper sample preparation is also important since clean samples can minimize the interference from co-existing substances and improve the specificity and sensitivity of LC-MS/MS assays. A combination of different methods can be utilized to improve bioanalytical performance and ensure more accurate quantification. This review provides an overview of various protein assays and sample preparation methods, with particular emphasis on quantitative protein analysis by LC-MS/MS.
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Affiliation(s)
- Jae Geun Song
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Kshitis Chandra Baral
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Gyu-Lin Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Ji-Won Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Soo-Hwa Seo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Da-Hyun Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Dong Hoon Jung
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Nonye Linda Ifekpolugo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Hyo-Kyung Han
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
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4
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Mass spectrometry-based multi-attribute method for mutation analysis in the early development of therapeutic proteins. J Pharm Biomed Anal 2022; 220:115018. [PMID: 36030755 DOI: 10.1016/j.jpba.2022.115018] [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: 05/01/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/22/2022]
Abstract
The early intervention is essential, and later development cannot compensate for this initial generation of an antibody drug. Especially for sequence variants (SVs), should cause concern during the early bioprocess development. The advancement of bioprocess development is paralleled by development of state-of-the-art analytical methods that will provide further information. In the present study, a mass spectrometry (MS)-based multi-attribute method (MAM) was used to simultaneously monitor the SVs and other quality attributes in the early bioprocess development of ofatumumab, and a sequence variant (SV) was detected by a subunit-based MAM. Subsequently, the variant was further identified by MS/MS and confirmed by adding a synthetic peptide. Furthermore, the content of the SV was detected via DNA sequencing. The levels of the variant (T175A mutant) in the light chain were demonstrate to be nearly consistent at the DNA and protein levels, suggesting that the mutation may have negligible effect on both the transcriptional and translational levels. Collectively, these results indicate that broad-spectrum, rapid, and accurate platform such as MS-based MAM should be implemented to quality control for the early development of therapeutic proteins, it will also be important to establish an effective and integrated MAM to control SVs during therapeutic proteins development.
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5
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Abstract
Drug analysis represents a large field in different disciplines. Plasma is commonly considered to be the biosample of choice for that purpose. However, concentrations often do not represent the levels present within deeper compartments and therefore cannot sufficiently explain efficacy or toxicology of drugs. MALDI-MS in drug analysis is of great interest for high-throughput quantification and particularly spatially resolved tissue imaging. The current perspective article will deal with challenges and opportunities of MALDI-MS drug analysis in different biological samples. A particular focus will be on hair samples. Recent applications were included, reviewed for their instrumental setup and sample preparation and pros and cons as well as future perspectives are critically discussed.
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6
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Biswas S, Rolain JM. Use of MALDI-TOF mass spectrometry for identification of bacteria that are difficult to culture. J Microbiol Methods 2013; 92:14-24. [DOI: 10.1016/j.mimet.2012.10.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 10/25/2012] [Accepted: 10/29/2012] [Indexed: 01/22/2023]
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7
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Ivanova B, Spiteller M. Gas-phase stabilized metal complexes of cyclic peptides – theoretical versus experimental study. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.676166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bojidarka Ivanova
- a Department of Environmental Chemistry and Analytical Chemistry, Faculty of Chemistry, Institute of Environmental Research, Dortmund University , Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Michael Spiteller
- a Department of Environmental Chemistry and Analytical Chemistry, Faculty of Chemistry, Institute of Environmental Research, Dortmund University , Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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8
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Croxatto A, Prod'hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012; 36:380-407. [DOI: 10.1111/j.1574-6976.2011.00298.x] [Citation(s) in RCA: 581] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/06/2011] [Accepted: 07/07/2011] [Indexed: 11/30/2022] Open
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9
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Banerjee R, Sudarslal S, Ranganayaki RS, Raghothama S. Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides. Org Biomol Chem 2011; 9:6234-45. [PMID: 21826329 DOI: 10.1039/c1ob05392b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical 'b-ion' series, exhibiting initial backbone cleavage explicitly at the β-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the 'b' or/and the 'y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the α-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the 'y-type'. Complementary NMR data showed that, while all metal ions were located around the β-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent β-hydroxy acid residue in isariins and the cis peptide bond in isaridins.
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Affiliation(s)
- Raja Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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10
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Tuñón J, Martín-Ventura JL, Blanco-Colio LM, Lorenzo Ó, López JA, Egido J. Proteomic Strategies in the Search of New Biomarkers in Atherothrombosis. J Am Coll Cardiol 2010; 55:2009-16. [DOI: 10.1016/j.jacc.2010.01.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/20/2010] [Accepted: 01/25/2010] [Indexed: 10/19/2022]
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11
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Chen Y, Le Droumaguet C, Li K, Cotham WE, Lee N, Walla M, Wang Q. A novel rearrangement of fluorescent human thymidylate synthase inhibitor analogues in ESI tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:403-410. [PMID: 20044271 DOI: 10.1016/j.jasms.2009.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/06/2009] [Accepted: 11/11/2009] [Indexed: 05/28/2023]
Abstract
Cu(I) catalyzed alkyne-azide cycloaddition reaction was employed to synthesize a series of anthracene-based human thymidylate synthase (hTS) inhibitor analogues. The triazolo-anthracene derivatives were characterized by ESI-MS/MS and a novel rearrangement reaction in ESI-MS/MS was observed. The mechanism is proposed whereby the protonated triazolo-anthracene derivative forms a carbocation, and then the carbocation electrophilically attacks an anthracene moiety resulting in formation of a rearrangement ion. Moreover, the carbocation prefers to attack the gamma position rather than the alpha or beta position of the anthracene moiety by an electrophilic substitution mechanism.
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Affiliation(s)
- Yi Chen
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
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12
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Wilson N, Simpson R, Cooper-Liddell C. Introductory glycosylation analysis using SDS-PAGE and peptide mass fingerprinting. Methods Mol Biol 2009; 534:205-212. [PMID: 19277550 DOI: 10.1007/978-1-59745-022-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Glycosylation is extremely complex, with the potential for a protein to have oligosaccharides attached at multiple sites, and for each site of glycosylation to have multiple structures attached to it. Structural information on the oligosaccharides bound to either asparagine residues (N-linked) or serine and threonine residues (O-linked) requires sensitive, specialised, and complex techniques and equipment. We show here, however, that a large amount of information regarding the glycosylation of glycoproteins can be obtained with common protein techniques such as 1D SDS-PAGE and peptide mass fingerprinting (PMF). Enzymatic deglycosylation in combination with SDS-PAGE and PMF analysis can determine the relative percentage of N-linked carbohydrate on the glycosylated protein, as well as attachment sites of the oligosaccharides.
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Affiliation(s)
- Nicole Wilson
- Apollo Cytokine Research, Beaconsfield, Sydney, NSW, Australia
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13
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Boonen K, Landuyt B, Baggerman G, Husson SJ, Huybrechts J, Schoofs L. Peptidomics: The integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis. J Sep Sci 2008; 31:427-45. [DOI: 10.1002/jssc.200700450] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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14
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Merkel P, Beck A, Muhammad K, Ali SA, Schönfeld C, Voelter W, Duszenko M. Spermine isolated and identified as the major trypanocidal compound from the snake venom of Eristocophis macmahoni causes autophagy in Trypanosoma brucei. Toxicon 2007; 50:457-69. [PMID: 17548100 DOI: 10.1016/j.toxicon.2007.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 04/12/2007] [Accepted: 04/13/2007] [Indexed: 01/10/2023]
Abstract
The snake venom from the leaf-nosed viper Eristocophis macmahoni was analyzed regarding its toxic effects on the bloodstream form of Trypanosoma brucei. A considerable trypanocidal effect was measured with an IC5 value of 186 ng/ml in bloodstream form parasites. Following several high performance liquid chromatography (HPLC) separation steps, the major trypanocidal activity was assigned to a single fraction by in vitro toxicity assays. Analysis by off-line ESI-MS(n) revealed an m/z value of 202.2 for the precursor ion and fragment ions of m/z=129.1 (MS2) and 112.1 (MS3), respectively, clearly corresponding to the molecular mass and the fragmentation pattern of the polyamine spermine. Quantification of spermine within the viper venom using an on-line hydrophilic interaction chromatography (HILIC) ESI-MS method revealed that this compound constituted approximately 1% of the dry venom mass. The polyamine oxidase activity in the fetal calf serum used for cultivation was responsible for a trypanocidal effect of pure spermine in the low micromolar range, whereas the antitrypanosomal activity of crude snake venom was virtually independent from serum, suggesting the oxidation of spermine by intrinsic venom components. Using fetal calf serum, spermine was shown to induce autophagy in the parasites using transmission electron microscopy (TEM).
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Affiliation(s)
- Patrick Merkel
- Interfaculty Institute for Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany
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15
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Williams SM, Siu KWM, Londry FA, Baranov VI. Study of the enhancement of dipolar resonant excitation by linear ion trap simulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:578-87. [PMID: 17188508 DOI: 10.1016/j.jasms.2006.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 10/11/2006] [Accepted: 10/16/2006] [Indexed: 05/13/2023]
Abstract
Resolution improvements in dipolar resonant excitation have been examined in a round-rod quadrupolar collision cell for values of the Mathieu characteristic exponent beta equal to n/p, where n and m are small integers (prime beta values) versus other beta values where n and p are not small (ordinary beta values). The trajectories of ions moving in the time-varying electric fields of a quadrupole with and without buffer-gas molecules were calculated to determine the relationship of prime and ordinary beta values to frequency resolution for resonant ion excitation and ejection. For prime beta values, the ion trajectory in the hyperbolic quadrupole field will be exactly periodic with a period of at most 4 pi p/Omega, where Omega is the angular frequency of the main drive radio-frequency (RF) potential. Ion trajectory simulations with prime beta versus ordinary beta values show that the motion of ions with prime beta values have simpler trajectories of shorter periods. Frequency response profiles (FRPs) for round-rod quadrupoles at zero pressure show that dipolar resonant excitations with prime beta values exhibit significantly narrower bandwidths than those with ordinary beta values. Simulations show that at 0.05 to 0.8 mTorr of nitrogen, it is possible to reduce the FRP bandwidth by 20% (measured at 50% depth).
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Affiliation(s)
- Sheldon M Williams
- Department of Chemistry, Center for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
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16
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Stigsnaes P, Frokjaer S, Bjerregaard S, van de Weert M, Kingshott P, Moeller EH. Characterisation and physical stability of PEGylated glucagon. Int J Pharm 2007; 330:89-98. [PMID: 17023127 DOI: 10.1016/j.ijpharm.2006.09.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 08/07/2006] [Accepted: 09/06/2006] [Indexed: 11/20/2022]
Abstract
Glucagon was mono-PEGylated with PEG 5000 at Lys-12 to examine the effect on conformation and physical stability during purification and freeze-drying. The model peptide glucagon is highly unstable and readily forms fibrils in solution. Secondary structure was determined by FTIR and far-UV CD and physical stability was assessed by the Thioflavin T assay. Glucagon samples were included, which underwent the same RP-HPLC purification and/or freeze-drying as glucagon-PEG 5000. After purification and freeze-drying glucagon samples showed formation of intermolecular beta-sheet by FTIR, this correlated with shorter lag-times for fibrillation in the Thioflavin T assay. Formation of intermolecular beta-sheet was less apparent for glucagon-PEG 5000 and no fibrillation was detected by Thioflavin T assay. Apparently PEGylation significantly improved the physical stability of glucagon after purification and freeze-drying, possibly by steric hindrance of peptide-peptide interactions. Alterations in the secondary structure were observed for freeze-dried and reconstituted peptide samples by liquid FTIR. The peak for alpha-helix shifted to 1664 cm(-1), which could possibly be explained by formation of 3(10)-helix. Neither 3(10)-helix nor intermolecular beta-sheet could be detected by far-UV CD, where all peptide samples showed similar spectra. In conclusion, glucagon-PEG 5000 showed a significantly improved physical stability during purification and freeze-drying compared to glucagon.
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Affiliation(s)
- Pernille Stigsnaes
- Department of Pharmaceutics, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, 2100 Copenhagen, Denmark.
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17
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Sleno L, Volmer DA. Toxin screening in phytoplankton: detection and quantitation using MALDI triple quadrupole mass spectrometry. Anal Chem 2007; 77:1509-17. [PMID: 15732938 DOI: 10.1021/ac0486600] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The investigation of a MALDI triple quadrupole instrument for the analysis of spirolide toxins in phytoplankton samples is described in this study. A high-frequency (kHz) laser was employed for MALDI, generating a semicontinuous ion beam, thus taking advantage of the high duty cycle obtained in sensitive triple quadrupole MRM experiments. Initially, several experimental parameters such as type of organic matrix and concentration, solvent composition, and matrix-to-analyte ratio were optimized, and their impact on sensitivity and precision of the obtained ion currents for a reference spirolide, 13-desmethyl-C, was studied. In all quantitative experiments, excellent linearities in the concentration range between 0.01 and 1.75 microg/mL were obtained, with R2 values of 0.99 or higher. The average precision of the quantitative MALDI measurements was 7.4+/-2.4% RSD. No systematic errors were apparent with this method as shown by a direct comparison to an electrospray LC/MS/MS method. Most importantly, the MALDI technique was very fast; each sample spot was analyzed in less than 5 s as compared to several minutes with the electrospray assay. To demonstrate the potential of the MALDI triple quadrupole method, its application to quantitative analysis in several different phytoplankton samples was investigated, including crude extracts and samples from mass-triggered fractionation experiments. 13-Desmethyl spirolide C was successfully quantified in these complex samples at concentration levels from 0.05 to 90.4 microg/mL (prior to dilution to have samples fall within the dynamic range of the method) without extensive sample preparation steps. The versatility of the MALDI triple quadrupole method was also exhibited for the identification of unknown spirolide analogues. Through the use of dedicated linked scan functions such as precursor ion and neutral loss scans, several spirolide compounds were tentatively identified directly from the crude extract, without the usual time-consuming chromatographic preseparation steps. Moreover, high-quality CID spectra were obtained for low-abundant spirolides present in the phytoplankton samples.
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MESH Headings
- Animals
- Chromatography, High Pressure Liquid
- Dinoflagellida/chemistry
- Heterocyclic Compounds, 3-Ring/analysis
- Heterocyclic Compounds, 3-Ring/chemistry
- Heterocyclic Compounds, 3-Ring/isolation & purification
- Hydrocarbons, Cyclic/analysis
- Hydrocarbons, Cyclic/chemistry
- Hydrocarbons, Cyclic/isolation & purification
- Imines/analysis
- Imines/chemistry
- Imines/isolation & purification
- Lactones/analysis
- Lactones/chemistry
- Lactones/isolation & purification
- Marine Toxins/analysis
- Marine Toxins/chemistry
- Marine Toxins/isolation & purification
- Molecular Structure
- Phytoplankton/chemistry
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Spiro Compounds/analysis
- Spiro Compounds/chemistry
- Spiro Compounds/isolation & purification
- Toxins, Biological/analysis
- Toxins, Biological/chemistry
- Toxins, Biological/isolation & purification
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Affiliation(s)
- Lekha Sleno
- Institute for Marine Biosciences, National Research Council, 1411 Oxford Street, Halifax, NS, Canada B3H 3Z1
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Catai JR, Toraño JS, de Jong GJ, Somsen GW. Capillary electrophoresis–mass spectrometry of proteins at medium pH using bilayer-coated capillaries. Analyst 2007; 132:75-81. [PMID: 17180183 DOI: 10.1039/b607178c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The feasibility of using noncovalently bilayer-coated capillaries for capillary electrophoresis-mass spectrometry (CE-MS) of acidic proteins was investigated using background electrolytes (BGEs) of medium pH. The capillary was coated by successively rinsing the capillary with solutions of the oppositely charged polymers polybrene (PB) and poly(vinyl sulfonic acid) (PVS). Volatile BGEs containing ammonium formate and/or N-methyl morpholine were tested at pH 7.5 and 8.5. Overall, these BGEs provided relatively fast protein separations (analysis times of ca. 12 min) and showed high efficiencies (70,000-300,000 plates) when the ionic strength was sufficiently high. Migration-time reproducibilities were very favorable with RSDs of less than 1.0%. Infusion experiments showed satisfactory MS responses for studied proteins dissolved in ammonium formate (pH 8.5), however, high concentrations of N-methyl morpholine appeared to seriously suppress the MS protein signals. Evaluation of the CE-MS system was performed by analyzing a mixture of intact proteins yielding efficient separations and good-quality mass spectra. CE-MS analysis of a reconstituted formulation of the biopharmaceutical recombinant human growth hormone (rhGH) which was stored for a prolonged time, revealed one degradation product which was provisionally identified as desamido rhGH. Based on the MS responses the amount of degradation was estimated to be ca. 25%.
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Affiliation(s)
- Jonatan R Catai
- Department of Biomedical Analysis, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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Casini A, Gabbiani C, Mastrobuoni G, Messori L, Moneti G, Pieraccini G. Exploring metallodrug-protein interactions by ESI mass spectrometry: the reaction of anticancer platinum drugs with horse heart cytochrome c. ChemMedChem 2006; 1:413-7. [PMID: 16892376 DOI: 10.1002/cmdc.200500079] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Angela Casini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto, Fiorentino, Italy
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Hernandez P, Müller M, Appel RD. Automated protein identification by tandem mass spectrometry: issues and strategies. MASS SPECTROMETRY REVIEWS 2006; 25:235-54. [PMID: 16284939 DOI: 10.1002/mas.20068] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated software identification of proteins from MS/MS data still faces a number of obstacles due to the complexity of the proteome or procedural issues of mass spectrometry data acquisition. Expected or unexpected modifications of the peptide sequences, polymorphisms, errors in databases, missed or non-specific cleavages, unusual fragmentation patterns, and single MS/MS spectra of multiple peptides of the same m/z are so many pitfalls for identification algorithms. A lot of research work has been carried out in recent years that yielded new strategies to handle a number of these issues. Multiple MS/MS identification algorithms are now available or have been theoretically described. The difficulty resides in choosing the most adapted method for each type of spectra being identified. This review presents an overview of the state-of-the-art bioinformatics approaches to the identification of proteins by MS/MS to help the reader doing the spade work of finding the right tools among the many possibilities offered.
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Shemesh D, Gerber RB. Classical Trajectory Simulations of Photoionization Dynamics of Tryptophan: Intramolecular Energy Flow, Hydrogen-Transfer Processes and Conformational Transitions. J Phys Chem A 2006; 110:8401-8. [PMID: 16821822 DOI: 10.1021/jp0570869] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One-photon and two-photon ionization dynamics of tryptophan is studied by classical trajectory simulations using the semiempirical parametric method number 3 (PM3) potential surface in "on the fly" calculations. The tryptophan conformer is assumed to be in the vibrational ground state prior to ionization. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for that state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. For the two-photon ionization process the ionization is assumed to go resonantively through the first excited state. Most trajectories are computed, and the analysis is carried out for the first 10 ps. A range of interesting effects are observed. The main findings are as follows: (1) Multiple conformational transitions are observed in most of the trajectories within the ultrafast duration of 10 ps. (2) Hydrogen transfer from the carboxyl group to the amino group and back has been observed. A zwitterion is formed as a transient state. (3) Two new isomers are formed during the dynamics, which have apparently not been previously observed. (4) Fast energy flow between the ring modes and the amino acid backbone is observed for both one- and two-photon ionization. However, the effective vibrational temperatures only approach the same value after 90 ps. The conformation transition dynamics, the proton-transfer processes and the vibrational energy flow are discussed and analyzed.
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Affiliation(s)
- Dorit Shemesh
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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Ethier M, Figeys D. Strategy to Design Improved Proteomic Experiments Based on Statistical Analyses of the Chemical Properties of Identified Peptides. J Proteome Res 2005; 4:2201-6. [PMID: 16335967 DOI: 10.1021/pr050290o] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomics is an emerging field that uses many types of proteomic platforms however has few standardized procedures. Deciding which platform to use to perform large-scale proteomic studies is either based on personal preference or on so-called "figures of merit" such as dynamic range, resolution, and the limit of detection; these factors are often insufficient to predict the outcome of the experiment as the detection of peptides correlates to the chemical properties of each peptide. There is a need for a novel figure of merit that describes the overall performance of a platform based on measured output, which in proteomics is often a list of identified peptides. We report the development of such a figure of merit based on a predictive genetic algorithm. This algorithm takes into account the properties of the observed peptides such as length, hydrophobicity, and pI. Several large-scale studies that differed in sample type or platform were used to demonstrate the usefulness of the algorithm for improved experimental design. The figures that were obtained were clustered to find platforms that were biased in similar ways. Even though some platforms are different, they lead to the identification of similar peptide types and are thus redundant. The algorithm can thus be used as an exploratory tool to suggest a minimal number of complementary experiments in order to maximize experimental efficiency.
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Rey S, Gardy JL, Brinkman FSL. Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria. BMC Genomics 2005; 6:162. [PMID: 16288665 PMCID: PMC1314894 DOI: 10.1186/1471-2164-6-162] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 11/17/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of a bacterial protein's subcellular localization (SCL) is important for genome annotation, function prediction and drug or vaccine target identification. Subcellular fractionation techniques combined with recent proteomics technology permits the identification of large numbers of proteins from distinct bacterial compartments. However, the fractionation of a complex structure like the cell into several subcellular compartments is not a trivial task. Contamination from other compartments may occur, and some proteins may reside in multiple localizations. New computational methods have been reported over the past few years that now permit much more accurate, genome-wide analysis of the SCL of protein sequences deduced from genomes. There is a need to compare such computational methods with laboratory proteomics approaches to identify the most effective current approach for genome-wide localization characterization and annotation. RESULTS In this study, ten subcellular proteome analyses of bacterial compartments were reviewed. PSORTb version 2.0 was used to computationally predict the localization of proteins reported in these publications, and these computational predictions were then compared to the localizations determined by the proteomics study. By using a combined approach, we were able to identify a number of contaminants and proteins with dual localizations, and were able to more accurately identify membrane subproteomes. Our results allowed us to estimate the precision level of laboratory subproteome studies and we show here that, on average, recent high-precision computational methods such as PSORTb now have a lower error rate than laboratory methods. CONCLUSION We have performed the first focused comparison of genome-wide proteomic and computational methods for subcellular localization identification, and show that computational methods have now attained a level of precision that is exceeding that of high-throughput laboratory approaches. We note that analysis of all cellular fractions collectively is required to effectively provide localization information from laboratory studies, and we propose an overall approach to genome-wide subcellular localization characterization that capitalizes on the complementary nature of current laboratory and computational methods.
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Affiliation(s)
- Sébastien Rey
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Jennifer L Gardy
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Fiona SL Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
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24
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Beck A, Bussat MC, Zorn N, Robillard V, Klinguer-Hamour C, Chenu S, Goetsch L, Corvaïa N, Van Dorsselaer A, Haeuw JF. Characterization by liquid chromatography combined with mass spectrometry of monoclonal anti-IGF-1 receptor antibodies produced in CHO and NS0 cells. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 819:203-18. [PMID: 15833284 DOI: 10.1016/j.jchromb.2004.06.052] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Revised: 06/07/2004] [Accepted: 06/21/2004] [Indexed: 11/26/2022]
Abstract
7H2HM is a new humanized recombinant monoclonal antibody (MAb) directed against insulin-like growth factor-1 receptor and produced in CHO cells. Homogeneity of intact antibody, reduced light and heavy chains, Fab and Fc fragments were investigated by analytical methods based on mass (SDS-PAGE, SEC), charge (IEF, C-IEX) and hydrophobicity differences (RP-HPLC, HIC) and compared side-by-side with A2CHM, produced in NS0 cells. Primary structures and disulfide bridge pairing were analyzed by microsequencing (Edman degradation), mass spectrometry (MALDI-TOF, ES-TOF) and peptide mapping after enzymatic digestion (Trypsin, endoprotease Lys-C, papain). The light chains demonstrated the expected sequences. The heavy chains yielded post-translational modifications previously reported for other recombinant humanized or human IgG1 such as N-terminal pyroglutamic acid, C-terminal lysine clipping and N-glycosylation for asparagine 297. More surprisingly, two-thirds of the 7H2HM heavy chains were shown to contain an additional 24-amino-acid sequence, corresponding to the translation of an intron located between the variable and the constant domains. Taken together these data suggest that 7H2HM is a mixture of three families of antibodies corresponding (i) to the expected structure (17%; 14,9297 Da; 1330 amino acids), (ii) a variant with a translated intron in one heavy chains (33%; 15,2878 Da; 1354 amino acids) and (iii) a variant with translated introns in two heavy chains (50%; 15,4459 Da; 1378 amino acids), respectively. RP-HPLC is not a commonly used chromatographic method to assess purity of monoclonal antibodies but unlike to SEC and SDS-PAGE, was able to show and to quantify the family of structures present in 7H2HM, which were also identified by peptide mapping, mass spectrometry and microsequencing.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/analysis
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Base Sequence
- CHO Cells
- Chromatography, High Pressure Liquid/methods
- Cricetinae
- Electrophoresis, Polyacrylamide Gel
- Insulin-Like Growth Factor I/immunology
- Molecular Sequence Data
- Peptide Mapping
- Protein Processing, Post-Translational
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Alain Beck
- Centre d'Immunologie Pierre Fabre, 5 Avenue Napoléon III, 74160 Saint-Julien-en-Genevois, France.
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25
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Sleno L, Volmer DA. Some fundamental and technical aspects of the quantitative analysis of pharmaceutical drugs by matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:1928-36. [PMID: 15954169 DOI: 10.1002/rcm.2006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The purpose of the present paper was to study some of the underlying physical and technical aspects of high-throughput quantitative matrix-assisted laser desorption/ionization (MALDI) of small drug molecules. A prototype MALDI-triple quadrupole instrument equipped with a high repetition rate laser was employed. Initially, the detection limits and dynamic ranges for the quantitation of four drugs (quinidine, danofloxacin, ramipril and nadolol) were determined. Internal standards were carefully chosen for each of these analytes in terms of structure similarity and fragmentation pathways. Three organic matrices were tested for these assays, resulting in different crystallization behaviors and measurement reproducibilities. alpha-Cyano-4-hydroxycinnamic acid yielded the best results and was subsequently employed for the quantitative determination of all four analytes. Further experiments considered the role of laser energy and pulse rate on the ablated areas as well as ion signals. Light microscope and scanning electron microscope images allowed the examination of the ablated area of the MALDI spots. The images showed convincing evidence that the ablated area was virtually void of crystals after analysis, with no preferential removal of material in the center of the laser's path. Average values for the amount of material ablated were determined to be 3.9+/-0.5% of the total spot size, and as low as 19.5 attomoles of analyte were detectable for our most sensitive analyte, ramipril. It was calculated that, under these assay conditions, it was possible to accurately quantify less than 1 femtomole of all analytes with the use of appropriately pure internal standards. These studies showed very promising results for the quantitative nature of MALDI for small molecules with molecular weights less than 500 Da.
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Affiliation(s)
- Lekha Sleno
- Institute for Marine Biosciences, National Research Council, 1411 Oxford St., Halifax, NS, Canada B3H 3Z1
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26
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Shemesh D, Chaban GM, Gerber RB. Photoionization Dynamics of Glycine: The First 10 Picoseconds. J Phys Chem A 2004. [DOI: 10.1021/jp040331o] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Dorit Shemesh
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel, NASA Ames Research Center, Mail Stop T27B-1, Moffett Field, California 94035, and Department of Chemistry, University of CaliforniaIrvine, Irvine, California 92697
| | - Galina M. Chaban
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel, NASA Ames Research Center, Mail Stop T27B-1, Moffett Field, California 94035, and Department of Chemistry, University of CaliforniaIrvine, Irvine, California 92697
| | - R. Benny Gerber
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel, NASA Ames Research Center, Mail Stop T27B-1, Moffett Field, California 94035, and Department of Chemistry, University of CaliforniaIrvine, Irvine, California 92697
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27
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Abstract
OBJECTIVE On July 9, 2003, the National Institutes of Health (NIH) released a new program announcement entitled "Proteomics in Auditory and Developmental Disease Processes." This initiative makes it clear that proteomic analysis in otology is a multi-year research priority for the NIH. The goal of this article is to describe the mechanics of modern proteomic techniques and review their applications in otology to date. DATA SOURCES General articles from the proteomic literature were used to construct a review of modern proteomic techniques. For literature on proteomics in otology, MEDLINE and CRISP databases were searched by various topics in otology and cross-referenced with principle proteomic technologies. STUDY SELECTION The criterion for selection was any study in otology that employs proteomic technology. CONCLUSIONS Incredible progress has been made in proteomic technology. However, modern proteomic techniques are currently underutilized in otologic research. The NIH proteomics initiative referenced above, in combination with an understanding of the basic tools of modern proteomic science, should help motivate otologists to discover innovative ways to apply modern proteomic techniques to specific problems in otology.
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Affiliation(s)
- John F McGuire
- University of California, Irvine, Department of Otolaryngology--Head and Neck Surgery, Irvine, California 92617, USA.
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Cargile BJ, Bundy JL, Stephenson JL. Potential for False Positive Identifications from Large Databases through Tandem Mass Spectrometry. J Proteome Res 2004; 3:1082-5. [PMID: 15473699 DOI: 10.1021/pr049946o] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biomedical research community at large is increasingly employing shotgun proteomics for large-scale identification of proteins from enzymatic digests. Typically, the approach used to identify proteins and peptides from tandem mass spectral data is based on the matching of experimentally generated tandem mass spectra to the theoretical best match from a protein database. Here, we present the potential difficulties of using such an approach without statistical consideration of the false positive rate, especially when large databases, as are encountered in eukaryotes are considered. This is illustrated by searching a dataset generated from a multidimensional separation of a eukaryotic tryptic digest against an in silico generated random protein database, which generated a significant number of positive matches, even when previously suggested score filtering criteria are used.
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Affiliation(s)
- Benjamin J Cargile
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709, USA
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29
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Williams SM, Brodbelt JS. MS(n) characterization of protonated cyclic peptides and metal complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1039-1054. [PMID: 15234363 DOI: 10.1016/j.jasms.2004.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Revised: 03/26/2004] [Accepted: 03/26/2004] [Indexed: 05/24/2023]
Abstract
MS(n) experiments involving low energy collisionally activated dissociation (CAD) in a quadrupole ion trap were used to characterize the fragmentation of alkali, alkaline earth and transition metal complexes of five cyclic peptides, and the results were compared with those obtained for protonated cyclic peptides. Complexes with metal ions produced enhanced abundances of the most diagnostic fragments for elucidating the primary structures. For cyclosporin A, nickel and lithium complexes gave additional sequence information compared with the protonated peptide. For depsipeptides, sodium and lead complexes were superior to the protonated peptide or other metal complexes for sequencing residues, and CAD of the lead complexes led to preferential cleavage of two residues at a time. For cyclic lipopeptides, complexes with silver, nickel and strontium ions provided enhanced abundances of key fragment ions.
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Affiliation(s)
- Sheldon M Williams
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 78712, USA
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30
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Millar AH. Location, location, location: surveying the intracellular real estate through proteomics in plants. FUNCTIONAL PLANT BIOLOGY : FPB 2004; 31:563-572. [PMID: 32688928 DOI: 10.1071/fp04034] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 03/16/2004] [Indexed: 06/11/2023]
Abstract
Knowledge of cellular compartmentation is critical to an understanding of many aspects of biological function in plant cells but it remains an under-emphasised concept in the use of and investment in plant functional genomic tools. The emerging effort in plant subcellular proteomics is discussed, and the current datasets that are available for a series of organelles and cellular membranes isolated from a range of plant species are noted. The benefit of knowing subcellular location in determining the role of proteins of unknown function is considered alongside the challenges faced in this endeavour. These include clear problems in dealing with contamination during the isolation of subcellular compartments, the meaningful integration of these datasets once completed to assemble a jigsaw of the cellular proteome as a whole, and the use of the wider literature in supplementing this proteomic discovery effort.
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Affiliation(s)
- A Harvey Millar
- Plant Molecular Biology Group, School of Biomedical and Chemical Sciences, The University of Western Australia, Crawley, WA 6009, Australia. Corresponding author; email
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31
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Sappl PG, Heazlewood JL, Millar AH. Untangling multi-gene families in plants by integrating proteomics into functional genomics. PHYTOCHEMISTRY 2004; 65:1517-1530. [PMID: 15276449 DOI: 10.1016/j.phytochem.2004.04.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 04/01/2004] [Indexed: 05/24/2023]
Abstract
The classification and study of gene families is emerging as a constructive tool for fast tracking the elucidation of gene function. A multitude of technologies can be employed to undertake this task including comparative genomics, gene expression studies, sub-cellular localisation studies and proteomic analysis. Here we focus on the growing role of proteomics in untangling gene families in model plant species. Proteomics can specifically identify the products of closely related genes, can determine their abundance, and coupled to affinity chromatography and sub-cellular fractionation studies, it can even provide location within cells and functional assessment of specific proteins. Furthermore global gene expression analysis can then be used to place a specific family member in the context of a cohort of co-expressed genes. In model plants with established reverse genetic resources, such as catalogued T-DNA insertion lines, this gene specific information can also be readily used for a wider assessment of specific protein function or its capacity for compensation through assessing whole plant phenotypes. In combination, these resources can explore partitioning of function between members and assess the level of redundancy within gene families.
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Affiliation(s)
- Pia G Sappl
- School of Biomedical and Chemical Sciences, The University of Western Australia, M310, Biochemistry, 35 Stirling Highway, Crawley, Perth 6009, WA, Australia
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32
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Wilson KE, Ryan MM, Prime JE, Pashby DP, Orange PR, O'Beirne G, Whateley JG, Bahn S, Morris CM. Functional genomics and proteomics: application in neurosciences. J Neurol Neurosurg Psychiatry 2004; 75:529-38. [PMID: 15026490 PMCID: PMC1739030 DOI: 10.1136/jnnp.2003.026260] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The sequencing of the complete genome for many organisms, including man, has opened the door to the systematic understanding of how complex structures such as the brain integrate and function, not only in health but also in disease. This blueprint, however, means that the piecemeal analysis regimes of the past are being rapidly superseded by new methods that analyse not just tens of genes or proteins at any one time, but thousands, if not the entire repertoire of a cell population or tissue under investigation. Using the most appropriate method of analysis to maximise the available data therefore becomes vital if a complete picture is to be obtained of how a system or individual cell is affected by a treatment or disease. This review examines what methods are currently available for the large scale analysis of gene and protein expression, and what are their limitations.
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Affiliation(s)
- K E Wilson
- MRC Building, Newcastle General Hospital, Westgate Road, Newcastle upon Tyne, UK
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33
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Yeboah FK, Konishi Y. Mass Spectrometry of Biomolecules: Functional Foods, Nutraceuticals, and Natural Health Products. ANAL LETT 2003. [DOI: 10.1081/al-120026571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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34
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Zhang L, Eugeni EE, Parthun MR, Freitas MA. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 2003; 112:77-86. [PMID: 12937907 DOI: 10.1007/s00412-003-0244-6] [Citation(s) in RCA: 200] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2003] [Revised: 05/22/2003] [Accepted: 05/23/2003] [Indexed: 10/26/2022]
Abstract
The extent and pattern of histone post-translational modifications is a key determinant dictating the structure of chromatin. We employed mass spectrometry to map the post-translational modifications present on mammalian core histones. Using accurate peptide mass fingerprinting on proteolytic digests of purified histones, we identified more than 20 novel sites of histone modification. One newly identified site of methylation, histone H4 lysine 59, maps to the surface of the nucleosome in close proximity to the site of the only identified histone core modification, histone H3 lysine 79. Consistent with the role of histone H3 lysine 79 methylation in the formation of silent chromatin structure, histone H4 lysine 59 is essential for transcriptional silencing at the yeast silent mating loci and telomeres.
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Affiliation(s)
- Liwen Zhang
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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35
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Lin D, Tabb DL, Yates JR. Large-scale protein identification using mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1646:1-10. [PMID: 12637006 DOI: 10.1016/s1570-9639(02)00546-0] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent achievements in genomics have created an infrastructure of biological information. The enormous success of genomics promptly induced a subsequent explosion in proteomics technology, the emerging science for systematic study of proteins in complexes, organelles, and cells. Proteomics is developing powerful technologies to identify proteins, to map proteomes in cells, to quantify the differential expression of proteins under different states, and to study aspects of protein-protein interaction. The dynamic nature of protein expression, protein interactions, and protein modifications requires measurement as a function of time and cellular state. These types of studies require many measurements and thus high throughput protein identification is essential. This review will discuss aspects of mass spectrometry with emphasis on methods and applications for large-scale protein identification, a fundamental tool for proteomics.
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Affiliation(s)
- Dayin Lin
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
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36
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Clerens S, D'Hondt E, Berghman LR, Vandesande F, Arckens L. Identification of cGnRH-II in the median eminence of Japanese quail (Coturnix coturnix japonica). Gen Comp Endocrinol 2003; 131:48-56. [PMID: 12620246 DOI: 10.1016/s0016-6480(02)00644-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In a previous paper, we described the presence of cGnRH-II in the quail (Coturnix coturnix japonica) and chicken (Gallus gallus) median eminence using highly specific antibodies directed against a polypeptide corresponding to the C-terminal portion of cGnRH-II (van Gils et al., 1993). This finding remained very controversial, since no other study, with any other antibody, had ever reported the presence of cGnRH-II immunoreactive fibers in the median eminence of birds. In this study, the cGnRH-II immunoreactive substances in quail median eminence were isolated by RP-HPLC and identified by RIA. To eliminate the possibility that the cGnRH-II-like immunoreactivity in the median eminence was due to a cross-reaction of our anti-cGnRH-II antiserum with an unknown peptide, the cGnRH-II immunoreactive substances, present in a quail median eminence extract, were isolated by immunoaffinity chromatography using immunoaffinity-purified antibodies. In the eluate of the immunoaffinity column only one peptide could be detected by mass spectrometry. This peptide had a mass of 1235.56 Da, which is the same as synthetic cGnRH-II. In addition, MS/MS fragmentation generated an amino acid sequence corresponding to the sequence of cGnRH-II. The present study therefore identified indisputably cGnRH-II in the median eminence of the quail.
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Affiliation(s)
- Stefan Clerens
- Laboratory of Neuroendocrinology and Immunological Biotechnology, Katholieke Universiteit Leuven, Naamsestraat 59, B-3000 Leuven, Belgium
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Abstract
The description of the human genome has opened new venues for the study and understanding of pathophysiological phenomena. In the 20th century, individual cell components were studied. The 21st century began with a global analysis of cell components. Thanks to the development of new technologies such as DNA chips, or two-dimensional electrophoresis, we can now study the expression of thousands of genes, or the proteins they encode, in a few hours. Genomics has opened the way for proteomics. Improved knowledge of genes does not provide information about cell functions, because any cell expresses all genes simultaneously. Instead, there is selective gene expression depending on the cell type and the stimuli to which it is exposed. The result of this is the proteome, an ensemble of proteins that are responsible for cell functions at any given moment, which are the object of the study of proteomics. The description of the proteome of cardiac cells has begun and some new proteins have been found to be dysregulated in different cardiomyopathies. These proteins are involved either in energy production or in the stress response, or belong to the cell proteasome or cytoskeleton. They may be potential risk markers or new therapeutic targets in the future. In this sense, chemogenomics is a new methodology for the development of new drugs using genomic and proteomic data.
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Affiliation(s)
- Fernando Vivanco
- Servicio de Inmunología. Fundación Jiménez Díaz. Madrid. España.
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Franz AH, Liu R, Song A, Lam KS, Lebrilla CB. High-throughput one-bead-one-compound approach to peptide-encoded combinatorial libraries: MALDI-MS analysis of single TentaGel beads. JOURNAL OF COMBINATORIAL CHEMISTRY 2003; 5:125-37. [PMID: 12625702 DOI: 10.1021/cc020083a] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification of pharmacologically promising compounds (lead compounds) from combinatorial libraries is frequently limited by the throughput of the analytical technique employed. Fourier transform mass spectrometry (FTMS) offers high sensitivity, mass accuracy (m/Deltam > 500 000), and sequencing capabilities. A rapid and efficient method for high-throughput analysis of single beads from peptide-encoded combinatorial libraries with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. Encoding peptides on single beads are identified and structurally characterized by MALDI time-of-flight (TOF) and ultrahigh-resolution MALDI Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. A strategy of on-probe sample preparation is developed to minimize handling of the beads.
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Affiliation(s)
- Andreas H Franz
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, USA
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Yao Y, Berg EA, Costello CE, Troxler RF, Oppenheim FG. Identification of protein components in human acquired enamel pellicle and whole saliva using novel proteomics approaches. J Biol Chem 2003; 278:5300-8. [PMID: 12444093 DOI: 10.1074/jbc.m206333200] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Precursor proteins of the acquired enamel pellicle derive from glandular and non-glandular secretions, which are components of whole saliva. The purpose of this investigation was to gain further insights into the characteristics of proteins in whole saliva and in vivo formed pellicle components. To maximize separation and resolution using only micro-amounts of protein, a two-dimensional gel electrophoresis system was employed. Protein samples from parotid secretion, submandibular/sublingual secretion, whole saliva, and pellicle were subjected to isoelectric focusing followed by SDS-PAGE. Selected protein spots were excised, subjected to "in-gel" trypsin digestion, and examined by mass spectrometry (MS). The data generated, including peptide maps and tandem MS spectra, were analyzed using protein data base searches. Components identified in whole saliva include cystatins (SA-III, SA, and SN), statherin, albumin, amylase, and calgranulin A. Components identified in pellicle included histatins, lysozyme, statherin, cytokeratins, and calgranulin B. The results showed that whole saliva and pellicle have more complex protein patterns than those of glandular secretions. There are some similarities and also distinct differences between the patterns of proteins present in whole saliva and pellicle. MS approaches allowed identification of not only well characterized salivary proteins but also novel proteins not previously identified in pellicle.
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Affiliation(s)
- Yuan Yao
- Department of Periodontology and Oral Biology, Boston University School of Dental Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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Kast J, Parker CE, van der Drift K, Dial JM, Milgram SL, Wilm M, Howell M, Borchers CH. Matrix-assisted laser desorption/ionization directed nano-electrospray ionization tandem mass spectrometric analysis for protein identification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1825-1834. [PMID: 12876682 DOI: 10.1002/rcm.1114] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In those cases where the information obtained by peptide mass fingerprinting or matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) is not sufficient for unambiguous protein identification, nano-electrospray ionization (nano-ESI) and/or electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis must be performed. The sensitivity of nano-ESI/MS, however, is lower than that of MALDI-MS, especially at very low analyte concentrations and/or in the presence of contaminants, such as salt and detergents. Moreover, to perform ESI-MS/MS, the peptide masses of the precursor ions must be known. The approach described in this paper, MALDI-directed nano-ESI-MS/MS, makes use of information obtained from the more sensitive MALDI-MS experiments in order to direct subsequent nano-ESI-MS/MS experiments. Peptide molecular ions found in the MALDI-MS analysis are then selected, as their (+2) precursor ions, for nano-ESI-MS/MS sequencing, even though these ions cannot be detected in the ESI-MS spectra. This method, originally proposed by Tempst et al. (Anal. Chem. 2000, 72: 777-790), has been extended to provide better sensitivity and shorter analysis times; also, a comparison with liquid chromatography/tandem mass spectrometry (LC/MS/MS) has been performed. These experiments, performed using quadrupole time-of-flight instruments equipped with commercially available nano-ESI sources, have allowed the unambiguous identification of in-gel digested proteins at levels below their ESI-MS detection limits, even in the presence of salts and detergents.
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Affiliation(s)
- Juergen Kast
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
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Abstract
This review focuses on biological and biomedical mass spectrometry, and covers a selection of publications in this area included in the MEDLINE database for the period 1987-2001. Over the last 15 years, biological and biomedical mass spectrometry has progressed out of all recognition. The development of soft ionization methods, such as electrospray ionization and matrix-assisted laser desorption ionization, has mainly contributed to the remarkable progress, because they can easily produce gas-phase ions of large, polar, and thermally labile biomolecules, such as proteins, peptides, nucleic acids and others. The innovations of ionization methods have led to remarkable progress in mass spectrometric technology and in biochemistry, biotechnology and molecular biology research. In addition, mass spectrometry is one of the powerful and effective technologies for drug discovery and development. It is applicable to studies on structural determination, drug metabolism, including pharmacokinetics and toxicokinetics, and de novo drug discovery by applying post-genomic approarches. In the present review, the innovative soft ionization methods are first discussed along with their features. Also, the characteristics of the mass spectrometers which are active in the biological and biomedical research fields are also described. In addition, examples of the applications of biological and biomedical mass spectrometry are provided.
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Affiliation(s)
- Nariyasu Mano
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980-8578, Japan.
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Takemoto M, Asker N, Gerhardt H, Lundkvist A, Johansson BR, Saito Y, Betsholtz C. A new method for large scale isolation of kidney glomeruli from mice. THE AMERICAN JOURNAL OF PATHOLOGY 2002; 161:799-805. [PMID: 12213707 PMCID: PMC1867262 DOI: 10.1016/s0002-9440(10)64239-3] [Citation(s) in RCA: 433] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Here we report a new isolation method for mouse glomeruli. The method is fast and simple and allows for the isolation of virtually all glomeruli present in the adult mouse kidney with minimal contamination of nonglomerular cells. Mice were perfused through the heart with magnetic 4.5- micro m diameter Dynabeads. Kidneys were minced into small pieces, digested by collagenase, filtered, and collected using a magnet. The number of glomeruli retrieved from one adult mouse was 20,131 +/- 4699 (mean +/- SD, n = 14) with a purity of 97.5 +/- 1.7%. The isolated glomeruli retained intact morphology, as confirmed by light and electron microscopy, as well as intact mRNA integrity, as confirmed by Northern blot analysis. The method was applicable also to newborn mice, which allows for the isolation of immature developmental stage glomeruli. This method makes feasible transcript profiling and proteomic analysis of the developing, healthy and diseased mouse glomerulus.
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Affiliation(s)
- Minoru Takemoto
- Department of Medical Biochemistry, Göteborg University, Sweden.
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Abstract
The publication of the human genome has presented the scientific community with an unprecedented amount of genetic information with the potential to revolutionize the drug discovery process. This information could be used to identify novel drug targets and disease markers or could aid in the development of personalized medicines. The realization that genetic changes must ultimately influence protein function has pushed the field of proteomics further into the limelight. In this review the applications of proteomics to the field of toxicology will be discussed. It is anticipated that, in the future, toxicologists will apply a range of genomic and proteomic techniques to address issues in toxicity.
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Affiliation(s)
- Lasantha R Bandara
- Oxford GlycoSciences (UK), The Forum, 86 Milton Park, Abingdon, UK OX14 4RY.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2447231 DOI: 10.1002/cfg.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:1324-1333. [PMID: 11754125 DOI: 10.1002/jms.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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