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Agregán R, Echegaray N, López-Pedrouso M, Kharabsheh R, Franco D, Lorenzo JM. Proteomic Advances in Milk and Dairy Products. Molecules 2021; 26:3832. [PMID: 34201770 PMCID: PMC8270265 DOI: 10.3390/molecules26133832] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 02/04/2023] Open
Abstract
Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes makes it also applicable to other areas of science. Milk is a highly heterogeneous and complex fluid, where there are numerous genetic variants and isoforms with post-translational modifications (PTMs). Due to the vast number of proteins and peptides existing in its matrix, proteomics is presented as a powerful tool for the characterization of milk samples and their products. The technology developed to date for the separation and characterization of the milk proteome, such as two-dimensional gel electrophoresis (2DE) technology and especially mass spectrometry (MS) have allowed an exhaustive characterization of the proteins and peptides present in milk and dairy products with enormous applications in the industry for the control of fundamental parameters, such as microbiological safety, the guarantee of authenticity, or the control of the transformations carried out, aimed to increase the quality of the final product.
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Affiliation(s)
- Rubén Agregán
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
| | - Noemí Echegaray
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
| | - María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain;
| | - Radwan Kharabsheh
- Business Administration, Faculty of Economics and Administrative Sciences, Applied Science University—Bahrain, Al Hidd 5055, Bahrain;
| | - Daniel Franco
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
| | - José M. Lorenzo
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
- Área de Tecnología de los Alimentos, Facultad de Ciencias de Ourense, Universidad de Vigo, 32004 Ourense, Spain
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Dorfer V, Strobl M, Winkler S, Mechtler K. MS Amanda 2.0: Advancements in the standalone implementation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9088. [PMID: 33759252 PMCID: PMC8244010 DOI: 10.1002/rcm.9088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/27/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Database search engines are the preferred method to identify peptides in mass spectrometry data. However, valuable software is in this context not only defined by a powerful algorithm to separate correct from false identifications, but also by constant maintenance and continuous improvements. METHODS In 2014, we presented our peptide identification algorithm MS Amanda, showing its suitability for identifying peptides in high-resolution tandem mass spectrometry data and its ability to outperform widely used tools to identify peptides. Since then, we have continuously worked on improvements to enhance its usability and to support new trends and developments in this fast-growing field, while keeping the original scoring algorithm to assess the quality of a peptide spectrum match unchanged. RESULTS We present the outcome of these efforts, MS Amanda 2.0, a faster and more flexible standalone version with the original scoring algorithm. The new implementation has led to a 3-5× speedup, is able to handle new ion types and supports standard data formats. We also show that MS Amanda 2.0 works best when using only the most common ion types in a particular search instead of all possible ion types. CONCLUSIONS MS Amanda is available free of charge from https://ms.imp.ac.at/index.php?action=msamanda.
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Affiliation(s)
- Viktoria Dorfer
- Bioinformatics Research GroupUniversity of Applied Sciences Upper AustriaSoftwarepark 11, 4232 HagenbergAustria
| | - Marina Strobl
- Bioinformatics Research GroupUniversity of Applied Sciences Upper AustriaSoftwarepark 11, 4232 HagenbergAustria
| | - Stephan Winkler
- Bioinformatics Research GroupUniversity of Applied Sciences Upper AustriaSoftwarepark 11, 4232 HagenbergAustria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)Campus‐Vienna‐Biocenter 1Vienna1030Austria
- Institute of Molecular Biotechnology (IMBA)Austrian Academy of Sciences, Vienna BioCenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
- Gregor Mendel Institute (GMI)Austrian Academy of Sciences, Vienna BioCenter (VBC)Dr. Bohr‐ Gasse 3Vienna1030Austria
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3
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Yoo HJ, Kim DH, Shin D, Oh Y, Lee S, Lee JY, Choi YJ, Lee SH, Lee KS, Kim Y, Cho K. Recent developments in pre-treatment and analytical techniques for synthetic polymers by MALDI-TOF mass spectrometry. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5767-5800. [PMID: 33241791 DOI: 10.1039/d0ay01729a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A great deal of effort has been expended to develop accurate means of determining the properties of synthetic polymers using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). Many studies have focused on the importance of sample pre-treatment to obtain accurate analysis results. This review discusses the history of synthetic polymer characterization and highlights several applications of MALDI-TOF MS that recognize the importance of pre-treatment technologies. The subject area is of significance in the field of analytical chemistry, especially for users of the MALDI technique. Since the 2000s, many such technologies have been developed that feature improved methods and conditions, including solvent-free systems. In addition, the recent diversification of matrix types and the development of carbon-based matrix materials are described herein together with the current status and future directions of MALDI-TOF MS hardware and software development. We provide a summary of processes used for obtaining the best analytical results with synthetic polymeric materials using MALDI-TOF MS.
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Affiliation(s)
- Hee-Jin Yoo
- Center for Research Equipment, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28119, Korea.
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4
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A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field. Proteomes 2020; 8:proteomes8030014. [PMID: 32640657 PMCID: PMC7564415 DOI: 10.3390/proteomes8030014] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.
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5
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Proteomic Response of Host Plants to Citrus tristeza virus. Methods Mol Biol 2019. [PMID: 31222706 DOI: 10.1007/978-1-4939-9558-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteomics is an excellent technique for detecting proteins involved in plant responses infected with the Citrus tristeza virus. Here we describe the process to extract proteins to obtain two-dimensional gels with a large number of spots, well distributed, and with good quality. The extraction process that associates successive washes with ultrasonication steps proved to be efficient for the detection of proteins. With this technique it was possible to obtain clear gels which were detected in about 600 spots distributed throughout the gel without the presence of drag.
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6
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Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. ACTA ACUST UNITED AC 2014; 108:10.21.1-10.21.30. [PMID: 25271712 DOI: 10.1002/0471142727.mb1021s108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.
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Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York
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7
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Protein fractionation and detection for metalloproteomics: challenges and approaches. Anal Bioanal Chem 2012; 402:3311-22. [DOI: 10.1007/s00216-012-5743-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/09/2012] [Accepted: 01/12/2012] [Indexed: 12/17/2022]
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8
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Zhang D, Liu H, Zhang S, Chen X, Li S, Zhang C, Hu X, Bi K, Chen X, Jiang Y. An effective method for de novo peptide sequencing based on phosphorylation strategy and mass spectrometry. Talanta 2011; 84:614-22. [DOI: 10.1016/j.talanta.2010.12.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
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9
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Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. ACTA ACUST UNITED AC 2011; Chapter 16:Unit16.1. [PMID: 21104985 DOI: 10.1002/0471140864.ps1601s62] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.
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Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York, USA
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10
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Protein identification from two-dimensional gel electrophoresis by connecting ZipTip with a home-assembled nanoflow system. Mikrochim Acta 2010. [DOI: 10.1007/s00604-010-0399-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Advance of Peptide Detectability Prediction on Mass Spectrometry Platform in Proteomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.3724/sp.j.1096.2010.00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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XU CM, ZHANG JY, LIU H, SUN HC, ZHU YP, XIE HW. Advance of Peptide Detectability Prediction on Mass Spectrometry Platform in Proteomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60023-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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van Breukelen B, Georgiou A, Drugan MM, Taouatas N, Mohammed S, Heck AJR. LysNDeNovo
: An algorithm enabling de novo
sequencing of Lys-N generated peptides fragmented by electron transfer dissociation. Proteomics 2010; 10:1196-201. [DOI: 10.1002/pmic.200900405] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Zhu X, Anderson VE, Sayre LM. Charge-derivatized amino acids facilitate model studies on protein side-chain modifications by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2113-2124. [PMID: 19517464 PMCID: PMC2902170 DOI: 10.1002/rcm.4116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The alpha-amino groups of histidine and lysine were derivatized with p-carboxylbenzyltriphenylphosphonium to form the pseudo dipeptides, PHis and PLys, which can be sensitively detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) due to the fixed positive charge of the phosphonium group. Detection limits of PHis and PLys by MALDI-TOFMS were both 30 fmol with a signal-to-noise ratio of 5:1. These pseudo dipeptides were excellent surrogates for His- or Lys-containing peptides in model reactions mimicking proteins with reactive electrophiles, prominently those generated by peroxidation of polyunsaturated fatty acids including 4-hydroxy-2(E)-nonenal (HNE), 4-oxo-2(E)-nonenal (ONE), 2(E)-octenal, and 2(E)-heptenal. An air-saturated solution of linoleic acid (d0:d5 = 1:1) was incubated in the presence of Fe(II) and ascorbate with these two pseudo dipeptides, and the reaction products were characterized by MALDI-TOFMS and liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS). By using PHis and PLys, the previously reported ONE-derived His-furan adduct was detected along with evidence for a cyclic alpha,beta-unsaturated ketone. A dimer formed from ONE was found to react with PHis through Michael addition. Alkenals were found to form two novel adducts with PLys. 2(E)-Octenoic acid-His Michael adduct and N(epsilon)-pentanoyllysine were identified as potential protein side-chain adducts modified by products of linoleic acid peroxidation. In addition, when PHis or PLys and AcHis or BocLys were exposed to the linoleic acid peroxidation, an epoxy-keto-ocatadecenoic acid mediated His-His cross-link was detected, along with the observation of a His-ONE/9,12-dioxo-10-dodecenoic acid-Lys derived pyrrole cross-link.
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Affiliation(s)
- Xiaochun Zhu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Vernon E. Anderson
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Lawrence M. Sayre
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
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15
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Analysis of angiotensin II receptor antagonist and protein markers at microliter level plasma by LC–MS/MS. J Pharm Biomed Anal 2009; 49:123-8. [DOI: 10.1016/j.jpba.2008.09.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Revised: 09/27/2008] [Accepted: 09/30/2008] [Indexed: 11/20/2022]
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16
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Boersema PJ, Taouatas N, Altelaar AFM, Gouw JW, Ross PL, Pappin DJ, Heck AJR, Mohammed S. Straightforward and de novo peptide sequencing by MALDI-MS/MS using a Lys-N metalloendopeptidase. Mol Cell Proteomics 2008; 8:650-60. [PMID: 19043101 DOI: 10.1074/mcp.m800249-mcp200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, we explore the potential of the metalloendopeptidase Lys-N for MALDI-MS/MS proteomics applications. Initially we digested a HEK293 cellular lysate with Lys-N and, for comparison, in parallel with the protease Lys-C. The resulting peptides were separated by strong cation exchange to enrich and isolate peptides containing a single N-terminal lysine. MALDI-MS/MS analysis of these peptides yielded CID spectra with clear and often complete sequence ladders of b-ions. To test the applicability for de novo sequencing we next separated an ostrich muscle tissue protein lysate by one-dimensional SDS-PAGE. A protein band at 42 kDa was in-gel digested with Lys-N. Relatively straightforward sequencing resulted in the de novo identification of the two ostrich proteins creatine kinase and actin. We therefore conclude that this method that combines Lys-N, strong cation exchange enrichment, and MALDI-MS/MS analysis provides a valuable alternative proteomics strategy.
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Affiliation(s)
- Paul J Boersema
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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17
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Pandhal J, Wright PC, Biggs CA. Proteomics with a pinch of salt: a cyanobacterial perspective. SALINE SYSTEMS 2008; 4:1. [PMID: 18412952 PMCID: PMC2386806 DOI: 10.1186/1746-1448-4-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 04/15/2008] [Indexed: 11/10/2022]
Abstract
Cyanobacteria are ancient life forms and have adapted to a variety of extreme environments, including high salinity. Biochemical, physiological and genetic studies have contributed to uncovering their underlying survival mechanisms, and as recent studies demonstrate, proteomics has the potential to increase our overall understanding further. To date, most salt-related cyanobacterial proteomic studies have utilised gel electrophoresis with the model organism Synechocystis sp. PCC6803. Moreover, focus has been on 2-4% w/v NaCl concentrations within different cellular compartments. Under these conditions, Synechocystis sp. PCC6803 was found to respond and adapt to salt stress through synthesis of general and specific stress proteins, altering the protein composition of extracellular layers, and re-directing control of complex central intermediary pathways. Post-transcriptional control was also predicted through non-correlating transcript level data and identification of protein isoforms.In this paper, we also review technical developments with emphasis on improving the quality and quantity of proteomic data and overcoming the detrimental effects of salt on sample preparation and analysis. Developments in gel-free methods include protein and peptide fractionation workflows, which can increase coverage of the proteome (20% in Synechocystis sp. PCC6803). Quantitative techniques have also improved in accuracy, resulting in confidence in quantitation approaching or even surpassing that seen in transcriptomic techniques (better than 1.5-fold in differential expression). Furthermore, in vivo metabolic labelling and de novo protein sequencing software have improved the ability to apply proteomics to unsequenced environmental isolates. The example used in this review is a cyanobacterium isolated from a Saharan salt lake.
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Affiliation(s)
- Jagroop Pandhal
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Phillip C Wright
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Catherine A Biggs
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
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18
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Sanders ME, Dias EC, Xu BJ, Mobley JA, Billheimer D, Roder H, Grigorieva J, Dowsett M, Arteaga CL, Caprioli RM. Differentiating proteomic biomarkers in breast cancer by laser capture microdissection and MALDI MS. J Proteome Res 2008; 7:1500-7. [PMID: 18386930 DOI: 10.1021/pr7008109] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We assessed proteomic patterns in breast cancer using MALDI MS and laser capture microdissected cells. Protein and peptide expression in invasive mammary carcinoma versus normal mammary epithelium and estrogen-receptor positive versus estrogen-receptor negative tumors were compared. Biomarker candidates were identified by statistical analysis and classifiers were developed and validated in blinded test sets. Several of the m/ z features used in the classifiers were identified by LC-MS/MS and two were confirmed by immunohistochemistry.
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Affiliation(s)
- Melinda E Sanders
- Department of Pathology, Vanderbilt University, Nashville, Tennessee 37232, USA.
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19
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Bunger MK, Cargile BJ, Ngunjiri A, Bundy JL, Stephenson JL. Automated Proteomics of E. coli via Top-Down Electron-Transfer Dissociation Mass Spectrometry. Anal Chem 2008; 80:1459-67. [DOI: 10.1021/ac7018409] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maureen K. Bunger
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Benjamin J. Cargile
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Anne Ngunjiri
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Jonathan L. Bundy
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - James L. Stephenson
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
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20
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Nice EC, Rothacker J, Weinstock J, Lim L, Catimel B. Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis. J Chromatogr A 2007; 1168:190-210; discussion 189. [PMID: 17597136 DOI: 10.1016/j.chroma.2007.06.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 01/09/2023]
Abstract
The routine detection of low abundance components in complex samples for detailed proteomics analysis continues to be a challenge. Whilst the potential of multidimensional chromatographic fractionation for this purpose has been proposed for some years, and was used effectively for the purification to homogeneity of trace components in bulk biological samples for N-terminal sequence analysis, its practical application in the proteomics arena is still limited. This article reviews some of the recent data using these approaches, including the use of microaffinity purification as part of multidimensional protocols for downstream proteomics analysis.
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Affiliation(s)
- E C Nice
- Protein Biosensing and Epithelial Laboratories, Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, P.O. Royal Melbourne Hospital, Parkville, Vic. 3050, Australia.
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21
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Lu CY, Wu CY, Lin CH. Protein identification by syringe pump-driven reversed-phase LC-MS/MS. Anal Biochem 2007; 368:123-9. [PMID: 17662228 DOI: 10.1016/j.ab.2007.06.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 01/26/2007] [Indexed: 11/26/2022]
Abstract
In typical mass spectrometry-based protein identification using peptide fragmentation fingerprinting, front-end separation plays a critical role in successful peptide sequencing. This separation step demands a great deal of time and usually is the rate-limiting step for the whole process. Here we provide an alternative separation method, based on a simple nanoflow delivery system, that is able to shorten the separation time considerably. This system consists of a 25-mul syringe connected to a manually packed reversed-phase mini-capillary column that can be directly coupled to an electrospray ionization tandem mass spectrometer. A syringe pump is then used to deliver the peptide mixtures at a nanoscale flow rate. We examined the efficiency and efficacy of this method by analyzing the tryptic peptides of bovine serum albumin and of 10 Escherichia coli proteins separated by two-dimensional gel electrophoresis (2DE). The results showed that identification of each protein could be achieved successfully within 25 min by using the disposable mini-capillary column. Moreover, all 2DE-separated E. coli proteins were identified at high confidence levels. Together, our data suggest that this method is a suitable option for mass spectrometry-based protein identification.
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Affiliation(s)
- Chi-Yu Lu
- Proteome Research Center, National Yang-Ming University, Taipei 11221, Taiwan
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22
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Hasegawa T, Wakita Y, Zhu Y, Matsuura H, Haraguchi H, Umemura T. Speciation of Human Serum Proteins Based on Trace Metal Mapping Analysis by CIM Monolithic Disk Column HPLC/ICP-MS in Complement with Off-Line MALDI-TOF-MS Analysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.503] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
A huge number of genes within the human genome code for proteins that mediate and/or control nutritional processes. Although a large body of information on the number of genes, on chromosomal localisation, gene structure and function has been gathered, we are far from understanding the orchestrated way of how they make metabolism. Nevertheless, based on the genetic information emerging on a daily basis, we are offered fantastic new tools that allow us new insights into the molecular basis of human metabolism under normal as well as pathophysiological conditions. Recent technological advancements have made it possible to analyse simultaneously large sets of mRNA and/or proteins expressed in a biological sample or to define genetic heterogeneity that may be important for the individual response of an organism to changes in its nutritional environment. Applications of the new techniques of genome and proteome analysis are central for the development of nutritional sciences in the next decade and its integration into the rapidly developing era of functional genomics.
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Dworzanski JP, Snyder AP. Classification and identification of bacteria using mass spectrometry-based proteomics. Expert Rev Proteomics 2007; 2:863-78. [PMID: 16307516 DOI: 10.1586/14789450.2.6.863] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Timely classification and identification of bacteria is of vital importance in many areas of public health. Mass spectrometry-based methods provide an attractive alternative to well-established microbiologic procedures. Mass spectrometry methods can be characterized by the relatively high speed of acquiring taxonomically relevant information. Gel-free mass spectrometry proteomics techniques allow for rapid fingerprinting of bacterial proteins using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or, for high-throughput sequencing of peptides from protease-digested cellular proteins, using mass analysis of fragments from collision-induced dissociation of peptide ions. The latter technique uses database searching of product ion mass spectra. A database contains a comprehensive list of protein sequences translated from protein-encoding open reading frames found in bacterial genomes. The results of such searches allow the assignment of experimental peptide sequences to matching theoretical bacterial proteomes. Phylogenetic profiles of sequenced peptides are then used to create a matrix of sequence-to-bacterium assignments, which are analyzed using numerical taxonomy tools. The results thereof reveal the relatedness between bacteria, and allow the taxonomic position of an investigated strain to be inferred.
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Affiliation(s)
- Jacek P Dworzanski
- Science Applications International Corporation (SAIC), PO Box 68, Aberdeen Proving Ground, MD 21010-0068, USA.
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25
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Lundgren C, Lahmann J, Becker S, Roblick U, Schedvins K, Boman K, Frankendal B, Nordström B, Auer G. 2-DE protein expression in endometrial carcinoma. Acta Oncol 2007; 45:685-94. [PMID: 16938811 DOI: 10.1080/02841860600660787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The objective of this study was to explore the protein expression pattern in normal endometrial mucosa (n = 5) and endometrial carcinoma (n = 15) of low (diploid) and high (aneuploid) malignancy potential by two-dimensional gel electrophoresis (2-DE). The specimens were evaluated for histopathologic subtype, stage and grade in relation to DNA ploidy. A match-set consisting of five samples from normal endometrium, eight diploid and seven aneuploid tumours was created. All the diploid and three of the aneuploid tumours were of endometrioid subtype, while the remaining four were of uterine seropapillary type. There were 192 protein spots differentiating diploid tumours from normal endometrium and 238 protein spots were separating aneuploid tumours from normal endometrium (p < 0.01). A cluster analysis based on 52 significantly deviating protein spots within the groups showed clustering and separation of the normal endometrium, diploid and aneuploid tumours. In conclusion this study showed significant differences in protein expression between normal endometrium and endometrial carcinoma as well as between endometrial carcinoma of low and high malignancy potential. In future studies these results may provide useful in finding new sensitive prognostic markers for endometrial cancer.
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Affiliation(s)
- Caroline Lundgren
- Department of Gynaecologic Oncology, Radiumhemmet, Institute of Oncology and Pathology, Karolinska University Hospital and Institute, Stockholm, Sweden.
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26
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Bisson LF, Karpel JE, Ramakrishnan V, Joseph L. Functional genomics of wine yeast Saccharomyces cerevisiae. ADVANCES IN FOOD AND NUTRITION RESEARCH 2007; 53:65-121. [PMID: 17900497 DOI: 10.1016/s1043-4526(07)53003-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The application of genomic technologies to the analysis of wine strains of Saccharomyces cerevisiae has greatly enhanced our understanding of both native and laboratory strains of this important model eukaryote. Not only are differences in transcript, protein, and metabolite profiles being uncovered, but the heritable basis of these differences is also being elucidated. Although some challenges remain in the application of functional genomic technologies to commercial and native strains of S. cerevisiae, recent improvements, particularly in data analysis, have greatly extended the utility of these tools. Comparative analysis of laboratory and wine isolates is refining our understanding of the mechanisms of genome evolution. Genomic analysis of Saccharomyces in native environments is providing evidence of gene function to previously uncharacterized open reading frames and delineating the physiological parameters of ecological niche specialization and stress adaptation. The wealth of information being generated will soon be utilized to construct commercial stains with more desirable phenotypes, traits that will be designed to be genetically stable under commercial production conditions.
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Affiliation(s)
- Linda F Bisson
- Department of Viticulture and Enology, University of California, Davis, California 95616, USA
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Zhang Z. De novo peptide sequencing based on a divide-and-conquer algorithm and peptide tandem spectrum simulation. Anal Chem 2006; 76:6374-83. [PMID: 15516130 DOI: 10.1021/ac0491206] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometry-based de novo peptide sequencing is generally more reliable on high-resolution instruments owing to their high resolution and mass accuracy. On a lower resolution instrument such as the more widely used quadrupole ion traps, de novo peptide sequencing is not so reliable or requires more MS(3) experiments. However, the peptide CID spectrum has been demonstrated to be quite reproducible on an ion trap instrument and can be predicted with good accuracy. A new de novo peptide sequencing technique, DACSIM, combining a divide-and-conquer algorithm for deriving sequence candidates and spectrum simulation for sequence refinement, is developed for spectra acquired on an ion trap instrument. When DACSIM was used to sequence peptides 500-1900 u in mass generated from proteolytic digests of hemoglobin and myoglobin, the success rate was 70% with a false positive rate of only 6%, when isoleucine and leucine residues were not distinguished.
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Affiliation(s)
- Zhongqi Zhang
- Analytical Sciences, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, USA.
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Corso TN, Van Pelt CK, Li J, Ptak C, Huang X. Ultralow-Volume Fraction Collection from NanoLC Columns for Mass Spectrometric Analysis of Protein Phosphorylation and Glycosylation. Anal Chem 2006; 78:2209-19. [PMID: 16579599 DOI: 10.1021/ac0517592] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An ultralow volume fraction collection system referred to as nano fraction analysis chip technology (nanoFACT) is reported. The system collects 25-2500-nL fractions from 75-microm nanoLC columns into pipet tips at a user-defined, timed interval, typically one fraction every 15-120 s. Following collection, the fractions in the tip dry down naturally on their own in such a way as to create a concentrated band at the very end of the interior of the pipet tip. The fractions are then reconstituted directly in the pipet tips in approximately 250 nL of solvent prior to analysis. Because the chromatography and reconstitution solvent are independent, the reconstitution solvent can be selected to maximize ionization efficiency without compromising chromatography. In the infusion analysis of the nanoLC fractions, a low-flow electrospray chip is used which consists of 400 nozzles, each with an inner diameter of 2.5 microm and yielding flow rates of approximately 20 nL/min. Therefore, when reconstituted in 250 nL, each nanoLC fraction can be analyzed for over 10 min. This increase in analysis time allows for signal averaging, resulting in higher data quality, collision energy optimization, slower scanning techniques to be used, such as neutral loss and precursor ion scanning, higher resolution scans on FTMS instruments, and improved peptide quantitation. Furthermore, the nanoLC fractions could be archived in the pipet tips for analysis at a later date. Here, the advantages of nanoFACT are shown for phosphorylation analysis using bovine fetuin and glycosylation analysis using bovine ribonuclease B (RNase B). In the phosphorylation analysis, a comparison between conventional nanoLC and a nanoFACT analysis was performed. An MS/MS spectrum of a triply phosphorylated peptide, 313-HTFSGVApSVEpSpSSGEAFHVGK-333 could only be obtained using nanoFACT, not with nanoLC. Furthermore, spectral quality for the nanoFACT analysis was significantly improved over nanoLC. This was determined by comparing the number of diagnostic ions between the nanoFACT and nanoLC spectra, and it was found that the nanoFACT spectra contained a 19% or greater number of diagnostic ions for nonphosphorylated peptides and 55% or greater for phosphorylated peptides. For the glycosylation analysis, the glycosylation site of RNase B was fully characterized using 100 fmol of tryptic digest on a three-dimensional ion trap mass spectrometer.
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Affiliation(s)
- Thomas N Corso
- Advion BioSystems, Inc., 30 Brown Road, Ithaca, New York 14850, USA.
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Lobiński R, Schaumlöffel D, Szpunar J. Mass spectrometry in bioinorganic analytical chemistry. MASS SPECTROMETRY REVIEWS 2006; 25:255-89. [PMID: 16273552 DOI: 10.1002/mas.20069] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A considerable momentum has recently been gained by in vitro and in vivo studies of interactions of trace elements in biomolecules due to advances in inductively coupled plasma mass spectrometry (ICP MS) used as a detector in chromatography and capillary and planar electrophoresis. The multi-isotopic (including non-metals such as S, P, or Se) detection capability, high sensitivity, tolerance to matrix, and large linearity range regardless of the chemical environment of an analyte make ICP MS a valuable complementary technique to electrospray MS and MALDI MS. This review covers different facets of the recent progress in metal speciation in biochemistry, including probing in vitro interactions between metals and biomolecules, detection, determination, and structural characterization of heteroatom-containing molecules in biological tissues, and protein monitoring and quantification via a heteroelement (S, Se, or P) signal. The application areas include environmental chemistry, plant and animal biochemistry, nutrition, and medicine.
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Affiliation(s)
- Ryszard Lobiński
- Equipe de Chimie Analytique Bio-Inorganique, CNRS UMR 5034, Hélioparc, 2, av. du Pr. Angot, F-64053 Pau, France.
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Hudelist G, Singer CF, Pischinger KID, Kaserer K, Manavi M, Kubista E, Czerwenka KF. Proteomic analysis in human breast cancer: Identification of a characteristic protein expression profile of malignant breast epithelium. Proteomics 2006; 6:1989-2002. [PMID: 16470630 DOI: 10.1002/pmic.200500129] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Gene expression analysis has become a promising tool in predicting the clinical course of malignant disease and the response to antineoplastic therapy. Surprisingly, only little is known about the protein expression pattern of human tumors. Recent advances in proteomic analysis allow proteins of interest to be identified by their expression and/or modification pattern in 2-DE rather than using the traditional approach of translating gene expression data. To identify a proteomic pattern that is characteristic for malignant breast epithelium, we performed differential 2-DE analysis in sets of microdissected malignant breast epithelia and corresponding adjacent normal breast epithelia from five patients with invasive breast carcinoma. Thirty-two protein spots were found to be selectively regulated in malignant epithelium, and were subjected to MALDI-TOF and/or immunoblotting for protein identification. Thirteen of the identified proteins had previously not been associated with breast cancer. The validity of these findings was confirmed by literature review and immunohistochemistry for identified proteins in an independent cohort of 50 breast cancer specimens. We here describe, for the first time, a proteomic analysis of matched normal and malignant epithelia from invasive breast carcinomas. This strategy leads to a better understanding of oncogenesis at an operational level and helps to characterize the malignant phenotype of individual tumors, and thereby to identify novel targets for antineoplastic therapy.
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Affiliation(s)
- Gernot Hudelist
- Division of Special Gynecology, Department of Obstetrics/Gynecology, Vienna Medical University, Vienna, Austria
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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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Warwood S, Mohammed S, Cristea IM, Evans C, Whetton AD, Gaskell SJ. Guanidination chemistry for qualitative and quantitative proteomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:3245-56. [PMID: 17019669 DOI: 10.1002/rcm.2691] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The application of guanidination chemistry, the conversion of lysine into homoarginine residues, is used to illustrate several important general considerations relating to the use of differential isotope labelling for relative quantification in proteomics. The derivatisation procedure has been optimised for automation using a liquid handling station designed for proteomics. Automated application of the procedure to the analysis of in-gel tryptic digests of multiple spots from the two-dimensional gel electrophoretic (2DE) analysis of proteins from the FDCP-mix cell line shows near-universal improvement in protein identification as a result of derivatisation. This chemistry has been extended for relative quantification, applicable to matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) and also tandem mass spectrometry (MS/MS). It provides a robust method for the quantitative comparison of two samples that have been separated by 2DE. A peptide pair may display poor detection during MS analysis, causing their reliable relative quantification to be difficult. In such circumstances, the additional selectivity of detection provided by MS/MS can substantiate identification and allow relative quantification of these species via product ion signal ratios.
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Affiliation(s)
- Stacey Warwood
- Michael Barber Centre for Mass Spectrometry and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7ND, UK
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Righetti PG, Castagna A, Antonucci F, Piubelli C, Cecconi D, Campostrini N, Rustichelli C, Antonioli P, Zanusso G, Monaco S, Lomas L, Boschetti E. Proteome analysis in the clinical chemistry laboratory: Myth or reality? Clin Chim Acta 2005; 357:123-39. [PMID: 15970281 DOI: 10.1016/j.cccn.2005.03.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 03/09/2005] [Indexed: 11/26/2022]
Abstract
BACKGROUND We review here modern aspects of proteomic analysis, as displayed via orthogonal mass/charge analysis (isoelectric focusing in the first dimension, followed by sodium dodecyl sulphate electrophoresis in polyacrylamide gels, SDS-PAGE, at right angles, in the second dimension). METHODS This technique is capable of displaying a few thousand polypeptide chains, characterized by a single pI and M(r) value as coordinates, and recognized via elution, digestion and mass spectrometry analysis. Although, up to the present, this technique has been used mostly for advanced research, with no immediate applications in the clinical chemistry laboratory, there are hints that such applications will soon become a reality. RESULTS AND CONCLUSIONS In the field of cancer research, it is here shown that stathmin (Op18) becomes heavily phosphorylated in cancerous mantle cell lymphomas and that the progression of the disease can be followed by the progression of phosphorylation of Op18 and by the appearance of additional phosphorylated spots. Also chemoresistance of different tumors has been evaluated via 2D-PAGE through quantitative, differential proteomics: among up- and down-regulated proteins in a human cervix squamous cell carcinoma cell line (A431), rendered resistant to cisplatin, one particular protein was found to appear in large quantities by de novo synthesis: 14-3-3, a protein known to impart resistance to apoptosis to cells. In the field of brain disorders, we could set up an easy test for detecting pathological prions in sporadic Creutzfeldt-Jakob disease (sCJD), by simply searching for those pathological forms in the olfactory mucosa (up to this finding, diagnosis could only be confirmed post-mortem). We are currently working on a test for differentiating sCJD from all the other degenerative dementias. Upon 2D mapping of cerebrospinal fluid (CSF) and immunoblot analysis, we could identify a major spot (pI 4.8, M(r) 30 kDa) followed by some two-three minor spots (pIs 5.0-6.0, same M(r) value) of the same 14-3-3 anti-apoptotic protein involved in chemoresistance. By this test, sCJD could be differentiated from all the other degenerative dementias, which are 14-3-3 negative (in sCJD, the rapid and massive brain cell damage releases large quantities of 14-3-3 in the cerebrospinal fluid). Another protein that appears very promising as a marker for sCJD is cystatin C, that is strongly up-regulated in this pathology. Human sera should also be mined for discovery of many more markers for disease. Up to the present, no one could be found, but this was due to the presence of several major proteins, obscuring all rare ones. Via several immuno-subtraction steps, followed by ion exchange and size exclusion chromatography, one can now detect proteins and peptides present in sera at levels below 10 ng/mL, highlighting the road to discovery of novel markers of disease. Another technique that could revolutionize biomarker discovery in biological fluids consists in the use of combinatorial beads to reduce the dynamic range. They consist in a library of combinatorial ligands coupled to small beads. Such a library comprises hexameric ligands composed of amino acids, resulting in millions different structures. When these beads are impregnated with complex proteomes (e.g., human sera, CSF, urines) of widely differing protein compositions, they are able to significantly reduce the concentration differences, thus greatly enhancing the possibility of evidencing low-abundance species.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Agricultural and Industrial Biotechnologies, University of Verona, Strada Le Grazie No. 15, Verona 37134, Italy.
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Wang H, Hanash S. Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry. MASS SPECTROMETRY REVIEWS 2005; 24:413-426. [PMID: 15389852 DOI: 10.1002/mas.20018] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The complexity of tissue and cell proteomes and the vast dynamic range of protein abundance present a formidable challenge for analysis that no one analytical technique can overcome. As a result, there is a need to integrate technologies to achieve the high-resolution and high-sensitivity analysis of complex biological samples. The combined technologies of separation science and biological mass spectrometry (Bio-MS) are the current workhorse in proteomics, and are continuing to evolve to meet the needs for high sensitivity and high throughput. They are relied upon for protein quantification, identification, and analysis of post-translational modifications (PTMs). The standard technique of two dimensional poly-acrylamide gel electrophoresis (2D PAGE) offers relatively limited resolution and sensitivity for the simultaneous analysis of all cellular proteins, with only the most highly abundant proteins detectable in whole cell or tissue-derived samples. Hence, many alternative strategies are being explored. Numerous sample preparation procedures are currently available to reduce sample complexity and to increase the detectability of low-abundance proteins. Maintaining proteins intact during sample preparation has important advantages compared with strategies that digest proteins at an early step. These strategies include the ability to quantitate and recover proteins, and the assessment of PTMs. A review of current intact protein-based strategies for protein sample preparation prior to mass spectrometry (MS) is presented in the context of biomedically driven applications.
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Affiliation(s)
- Hong Wang
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109-0656, USA
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35
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Feldmann J. What can the different current-detection methods offer for element speciation? Trends Analyt Chem 2005. [DOI: 10.1016/j.trac.2004.11.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
In mass spectrometry (MS)-based protein studies, peptide fragmentation analysis (i.e., MS/MS experiments such as matrix-assisted laser desorption ionization [MALDI]-post-source decay [PSD] analysis, collision-induced dissociation [CID] of electrospray- and MALDI-generated ions, and electron-capture and electron-transfer dissociation analysis of multiply charged ions) provide sequence information and, thus, can be used for (i) de novo sequencing, (ii) protein identification, and (iii) posttranslational or other covalent modification site assignments. This chapter offers a qualitative overview on which kind of peptide fragments are formed under different MS/MS conditions. High-quality PSD and CID spectra provide illustrations of de novo sequencing and protein identification. The MS/MS behavior of some common posttranslational modifications such as acetylation, trimethylation, phosphorylation, sulfation, and O-glycosylation is also discussed.
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37
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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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Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F. Bioinformatics support for high-throughput proteomics. J Biotechnol 2004; 106:147-56. [PMID: 14651857 DOI: 10.1016/j.jbiotec.2003.08.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteome data. The rapid advancement of this technique in combination with other methods used in proteomics results in an increasing number of high-throughput projects. This leads to an increasing amount of data that needs to be archived and analyzed. To cope with the need for automated data conversion, storage, and analysis in the field of proteomics, the open source system ProDB was developed. The system handles data conversion from different mass spectrometer software, automates data analysis, and allows the annotation of MS spectra (e.g. assign gene names, store data on protein modifications). The system is based on an extensible relational database to store the mass spectra together with the experimental setup. It also provides a graphical user interface (GUI) for managing the experimental steps which led to the MS data. Furthermore, it allows the integration of genome and proteome data. Data from an ongoing experiment was used to compare manual and automated analysis. First tests showed that the automation resulted in a significant saving of time. Furthermore, the quality and interpretability of the results was improved in all cases.
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Affiliation(s)
- Andreas Wilke
- Center for Genome Research, Bielefeld University, D-33594 Bielefeld, Germany.
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Brancia FL, Montgomery H, Tanaka K, Kumashiro S. Guanidino Labeling Derivatization Strategy for Global Characterization of Peptide Mixtures by Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2004; 76:2748-55. [PMID: 15144184 DOI: 10.1021/ac030421+] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Guanidination performed with isotopic isoforms of O-methylisourea was used in combination with reversed-phase liquid chromatography (LC) matrix-assisted laser desorption/ionization to characterize, both qualitatively and quantitatively, protein mixtures. Synthesis of (13)C- and (15)N(2)-labeled O-methylisourea sulfate produces a molecule that is 3 Da heavier than the light isotopic variant. Protein mixtures containing identical components in different concentration are pooled together following parallel derivatization. Relative quantification of protein mixtures is achieved by mass spectrometry. A difference of 3 Da allows negligible interference between the two isotopic clusters for quantification of peptides up to 1400 Da. Under these conditions, the chromatographic resolution achieved allows separation of different pairs of derivatized peptides without altering the retention time of structurally identical isotopic isoforms. Concomitant isolation of both chemically modified precursors is followed by tandem mass analysis. Activation of the ions via collisions with an inert gas produces isotopically derivatized fragment ions, which appear as doublets in the product ion spectrum. Since the modification occurs on the C-terminal lysine, ions incorporating the guanidino moiety on the C-terminus can be distinguished from those containing the original unmodified peptide N-terminus. Knowledge of the location of the proton can be beneficial to data interpretation and peptide sequencing.
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Affiliation(s)
- Francesco L Brancia
- Shimadzu Research Laboratory (Europe), Wharfside, Trafford Wharf Road, Manchester, M17 1GP, UK.
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Naylor S, Kumar R. Emerging role of mass spectrometry in structural and functional proteomics. ADVANCES IN PROTEIN CHEMISTRY 2004; 65:217-48. [PMID: 12964371 DOI: 10.1016/s0065-3233(03)01021-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Stephen Naylor
- Beyond Genomics, Inc., Waltham, Massachusetts 02451, USA
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Schwartz SA, Weil RJ, Johnson MD, Toms SA, Caprioli RM. Protein Profiling in Brain Tumors Using Mass Spectrometry. Clin Cancer Res 2004; 10:981-7. [PMID: 14871976 DOI: 10.1158/1078-0432.ccr-0927-3] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The purpose of this research was to perform a preliminary assessment of protein patterns in primary brain tumors using a direct-tissue mass spectrometric technique to profile and map biomolecules. EXPERIMENTAL DESIGN We examined 20 prospectively collected, snap-frozen normal brain and brain tumor specimens using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), and compared peptide and protein expression in primary brain tumor and nontumor brain tissues. RESULTS MS can be used to identify protein expression patterns in human brain tissue and tumor specimens. The mass spectral patterns can reliably identify glial neoplasms of similar histological grade and differentiate them from tumors of different histological grades as well as from nontumor brain tissues. Initial bioinformatics cluster analysis algorithms classified tumor and nontumor tissues into similar groups comparable with their histological grade. CONCLUSIONS We describe a novel tool for the analysis of protein expression patterns in human glial neoplasms. Initial results demonstrate that MALDI-MS technology can significantly aid in the process of unraveling and understanding the molecular complexities of gliomas. MALDI-MS accurately and reliably identified normal and neoplastic tissues, and could be used to discriminate between tumors of increasing grades.
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Affiliation(s)
- Sarah A Schwartz
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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Ruiz Encinar J, Polatajko A, Szpunar J, Łobinski R. Identification of non-peptide species in selenized yeast by MALDI mass spectrometry using post-source decay and orthogonal Q-TOF detection. Analyst 2004; 129:846-9. [PMID: 15343401 DOI: 10.1039/b406650b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential of tandem mass spectrometry following matrix-assisted laser desorption ionization (MALDI) was studied for speciation of selenium. Non-peptide selenium-containing compounds were isolated from a selenized yeast aqueous extract by size-exclusion chromatography. Post-source decay (PSD) was compared with orthogonal quadrupole collision cell dissociation for the purpose of obtaining fragmentation and structural information. In the PSD mode, the use of ion gate covering the whole isotopic cluster of the parent compound allowed the immediate recognition of fragments containing Se and those in which this element was absent. The tandem mass spectra obtained by orthogonal MALDI Q-TOF were equally informative in terms of the number of fragments but suffered from a poorer sensitivity. The mass accuracy was ca. 20 times better in the oMALDI configuration than in the PSD mode. An unknown selenium compound with an m/z 388 was detected with a mass accuracy of 3 ppm according to the proposed empiric formula.
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Affiliation(s)
- Jorge Ruiz Encinar
- Equipe de Chimie Analytique Bio-Inorganique, CNRS UMR 5034, Helioparc, 2, av. Pr. Angot, F-64053 Pau, France
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Wang W, Sun J, Nimtz M, Deckwer WD, Zeng AP. Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences. Proteome Sci 2003; 1:6. [PMID: 14653859 PMCID: PMC317362 DOI: 10.1186/1477-5956-1-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2003] [Accepted: 12/03/2003] [Indexed: 11/15/2022] Open
Abstract
Separation of proteins by two-dimensional gel electrophoresis (2-DE) coupled with identification of proteins through peptide mass fingerprinting (PMF) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is the widely used technique for proteomic analysis. This approach relies, however, on the presence of the proteins studied in public-accessible protein databases or the availability of annotated genome sequences of an organism. In this work, we investigated the reliability of using raw genome sequences for identifying proteins by PMF without the need of additional information such as amino acid sequences. The method is demonstrated for proteomic analysis of Klebsiella pneumoniae grown anaerobically on glycerol. For 197 spots excised from 2-DE gels and submitted for mass spectrometric analysis 164 spots were clearly identified as 122 individual proteins. 95% of the 164 spots can be successfully identified merely by using peptide mass fingerprints and a strain-specific protein database (ProtKpn) constructed from the raw genome sequences of K. pneumoniae. Cross-species protein searching in the public databases mainly resulted in the identification of 57% of the 66 high expressed protein spots in comparison to 97% by using the ProtKpn database. 10 dha regulon related proteins that are essential for the initial enzymatic steps of anaerobic glycerol metabolism were successfully identified using the ProtKpn database, whereas none of them could be identified by cross-species searching. In conclusion, the use of strain-specific protein database constructed from raw genome sequences makes it possible to reliably identify most of the proteins from 2-DE analysis simply through peptide mass fingerprinting.
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Affiliation(s)
- Wei Wang
- TU-BCE, GBF – German Research Centre for Biotechnology Mascheroder Weg 1, 38124 Braunschweig, Germany
| | - Jibin Sun
- Department of Genome Analysis, GBF – German Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
| | - Manfred Nimtz
- Department of Structure Study, GBF – German Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
| | - Wolf-Dieter Deckwer
- TU-BCE, GBF – German Research Centre for Biotechnology Mascheroder Weg 1, 38124 Braunschweig, Germany
| | - An-Ping Zeng
- Department of Genome Analysis, GBF – German Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
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Cristoni S, Bernardi LR. Development of new methodologies for the mass spectrometry study of bioorganic macromolecules. MASS SPECTROMETRY REVIEWS 2003; 22:369-406. [PMID: 14528493 DOI: 10.1002/mas.10062] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution.
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Affiliation(s)
- Simone Cristoni
- Università degli Studi di Milano, Centro Interdisciplinare Studi Bio-molecolari e Applicazioni Industriali CISI, Via Fratelli Cervi 93, 20090 Segrate Milano, Italy.
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45
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Nouwens AS, Walsh BJ, Cordwell SJ. Application of proteomics to Pseudomonas aeruginosa. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2003; 83:117-40. [PMID: 12934928 DOI: 10.1007/3-540-36459-5_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The recent completion of the Pseudomonas Genome Project, in conjunction with the Pseudomonas Community Annotation Project (PseudoCAP) has fast-tracked our ability to apply the tools encompassed under the term 'proteomics' to this pathogen. Such global approaches will allow the research community to answer long-standing questions regarding the ability of Pseudomonas aeruginosa to survive diverse habitats, its high intrinsic resistance to antibiotics and its pathogenic nature towards humans. Proteomics provides an array of tools capable of confirming the expression of Open Reading Frames (ORF), the relative levels of their expression, the environmental conditions required for this expression and the sub-cellular location of the encoded gene-products. Since proteins are important cellular effectors, the biological questions we pose can be defined in terms of changes in protein expression detectable by separation to purity using two-dimensional gel electrophoresis (2-DGE) and relation to gene sequences via mass spectrometry. As such, we can compare strains with well-characterized phenotypic differences, growth under a variety of stresses, protein interactions and complexes and aid in defining proteins of unknown function. While the complete genome has only recently been finished, a number of studies have already utilized this information and examined various protein gene-products using proteomics. This review summarizes the application of proteomics to P. aeruginosa and highlights potential areas of future research, including overcoming the traditional technical limitations associated with 2-DGE. More focused approaches that target sub-cellular fractions ('sub-proteomes') prior to 2-DGE can provide further functional information. A review of current and previous proteomic projects on P. aeruginosa is presented, as well as theoretical considerations of the importance of sub-proteomic approaches to enhance these investigations.
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46
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Abstract
Tandem mass spectrometry is becoming an increasingly important analytical technology in the clinical laboratory environment. Applications in toxicology and therapeutic drug monitoring have opened the door for tandem mass spectrometry and now we are seeing a vast array of new applications being developed. It has been the combination of tandem mass spectrometry with sample introduction techniques employing atmospheric pressure ionization that has enabled this technology to be readily implemented in the clinical laboratory. Although its major research applications started with pharmacology and proteomics, tandem mass spectrometry is being used for a great variety of analyses from steroids to catecholamines to peptides. As with chromatographic methods, tandem mass spectrometry is most cost effective when groups of compounds need to be measured simultaneously. However as the price/performance of this technology continues to improve, it will become even more widely utilized for clinical laboratory applications.
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Affiliation(s)
- Kent C Dooley
- Department of Pathology and Laboratory Medicine, IWK Health Centre and Department of Pathology, Dalhousie University Medical School, Halifax, Nova Scotia, Canada.
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Wittke S, Fliser D, Haubitz M, Bartel S, Krebs R, Hausadel F, Hillmann M, Golovko I, Koester P, Haller H, Kaiser T, Mischak H, Weissinger EM. Determination of peptides and proteins in human urine with capillary electrophoresis–mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J Chromatogr A 2003; 1013:173-81. [PMID: 14604118 DOI: 10.1016/s0021-9673(03)00713-1] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The on-line coupling of capillary electrophoresis (CE) with electrospray-time-of-flight mass spectrometry (MS) has been used to obtain patterns of peptides and proteins present in the urine of healthy human individuals. This led to the establishment of a "normal urine polypeptide pattern", consisting of 247 polypeptides, each of which was found in more than 50% of healthy individuals. Applying CE-MS to the analysis of urine of patients with kidney disease revealed differences in polypeptide pattern. Twenty-seven polypeptides were exclusively found in samples of patients. Another 13, present in controls, were missing. These data indicate that CE-MS can be applied as powerful tool in clinical diagnostics.
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Affiliation(s)
- Stefan Wittke
- Mosaiques Diagnostics and Therapeutics AG, Feodor-Lynen-Strasse 5, 30625 Hannover, Germany
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Encinar JR, Ouerdane L, Buchmann W, Tortajada J, Lobinski R, Szpunar J. Identification of Water-Soluble Selenium-Containing Proteins in Selenized Yeast by Size-Exclusion-Reversed-Phase HPLC/ICPMS Followed by MALDI-TOF and Electrospray Q-TOF Mass Spectrometry. Anal Chem 2003; 75:3765-74. [PMID: 14572042 DOI: 10.1021/ac034103m] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An approach to speciation of selenium incorporated in yeast proteins was developed. The tryptic digest of a water-soluble protein fraction isolated by size-exclusion chromatography was analyzed by reversed-phase HPLC/ICPMS. The selenopeptides selected owing to the detector's elemental specificity were then analyzed by MALDI-TOFMS in order to select target ions for collision-induced dissociation MS. The latter, carried out with an electrospray Q-TOF spectrometer, enabled the sequencing of the selenopeptides detected by HPLC/ICPMS. The approach allowed for the first time the identification of a family of Se-containing proteins resulting from the replacement by selenomethionine of 2-9 methionine residues in a salt-stress-induced protein SIP18 (Mr 8874). The presence of these proteins was confirmed by MALDI-TOFMS of the original (nondigested) protein fraction. Another selenium protein identified was a heat-shock protein HSP12 (Mr 11693) in which the only methionine residue was replaced by selenomethionine. These two Se-containing proteins accounted for more than 95% of selenium in the water-soluble protein fraction.
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49
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Moyer SC, VonSeggern CE, Cotter RJ. Fragmentation of cationized phosphotyrosine containing peptides by atmospheric pressure MALDI/Ion trap mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:581-592. [PMID: 12781459 DOI: 10.1016/s1044-0305(03)00142-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An investigation of phosphate loss from sodium-cationized phosphotyrosine containing peptide ions was conducted using liquid infrared (2.94 microm) atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI) coupled to an ion trap mass spectrometer (ITMS). Previous experiments in our laboratory explored the fragmentation patterns of protonated phosphotyrosine containing peptides, which experience a loss of 98 Da under CID conditions in the ITMS. This loss of 98 Da is unexpected for phosphotyrosine, given the structure of its side chain. Phosphate loss from phosphotyrosine residues seems to be dependent on the presence of arginine or lysine residues in the peptide sequence. In the absence of a basic residue, the protonated phosphotyrosine peptides do not undergo losses of HPO(3) (Delta 80 Da) nor HPO(3) + H(2)O (Delta 98 Da) in their CID spectra. However, sodium cationized phosphotyrosine containing peptides that do not contain arginine or lysine residues within their sequences do undergo losses of HPO(3) (Delta 80 Da) and HPO(3) + H(2)O (Delta 98 Da) in their CID spectra.
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Affiliation(s)
- Susanne C Moyer
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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50
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Smith DL, Evans CA, Pierce A, Gaskell SJ, Whetton AD. Changes in the proteome associated with the action of Bcr-Abl tyrosine kinase are not related to transcriptional regulation. Mol Cell Proteomics 2002; 1:876-84. [PMID: 12488463 DOI: 10.1074/mcp.m200035-mcp200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a hematopoietic stem cell disease, the hallmark of which is the Bcr-Abl protein tyrosine kinase (PTK). Without intervention the disease progresses from a benign chronic phase to a rapidly fatal blast crisis. To identify the molecular mechanisms underlying disease progression we used two-dimensional gel electrophoresis on a model we have previously described using the expression of a conditional mutant of Bcr-Abl PTK in a multipotent stem cell line, FDCP-Mix. Long term exposure of FDCP-Mix cells to Bcr-Abl mimics disease progression in CML. Four major differences were observed as a consequence of long term exposure to the Bcr-Abl PTK compared with cells exposed short term. The proteins were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry-generated peptide mass fingerprint data and liquid chromatography-tandem mass spectrometry-generated sequence information. Leukotriene A4 hydrolase, an enzyme known to be deregulated in CML, was found to be up-regulated. Annexin VI, vacuolar ATP synthase catalytic subunit A, and mortalin were found to be down-regulated. Poly(A) PCR cDNA analysis showed there was no correlation between the protein expression changes and mRNA levels. Western blot analysis also indicated no change in the levels of mortalin or leukotriene A4 hydrolase, indicating that post-translational events may modify protein content of the specific spots. Leukotriene B4 levels (product of leukotriene A4 hydrolase) were, however, reduced in cells exposed long term to Bcr-Abl activity. This study demonstrates the potential of proteomic analysis to define novel effects of oncogenes.
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Affiliation(s)
- Duncan L Smith
- Leukaemia Research Fund Cellular Development Unit, Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester, United Kingdom
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