Negative and positive ion matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and positive ion nano‐electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various <i>Bacillus</i> species

Bacher, Gerold; Körner, Roman; Atrih, Abdelmadjid; Foster, Simon J.; Roepstorff, Peter; Allmaier, Günter

doi:10.1002/jms.109

Cited by 24 publications

(19 citation statements)

References 75 publications

(104 reference statements)

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“…Samples were prepared according to a thin-layer method (Bacher et al, 2001). Briefly, 1 l of 0.2 M 2,5-dihydroxybenzoic acid (DHB) in 50% methanol was mixed on a sample plate with 1 l of sample and allowed to crystallize.…”

Section: Mass Spectral Identification Ofmentioning

confidence: 99%

Identification of differentially expressed proteins in human glioblastoma cell lines and tumors

Zhang

Tremblay

McDermid

et al. 2003

Glia

112

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KEY WORDSproteomics; matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF); liquid chromatography tandem mass spectrometry (LC-MS-MS); glioblastoma; U87MG; major vault protein; cystatin B; Hsp27; tissue transglutaminase; epidermal growth factor receptor ABSTRACT An in-frame deletion of 801 bp in exons 2-7 (type III mutation) of the epidermal growth factor receptor (EGFR) is detected at high incidence in primary glioblastoma tumors. A proteomic approach was used to generate differential protein expression maps of fetal human astrocytes (FHA), human glioblastoma cell lines U87MG and U87MG expressing type III EGFR deletion (U87MG⌬EGFR) that confers high malignancy to tumor cells. Two-dimensional gel electrophoresis followed by in-gel digestion of separated spots and protein identification by LC-MS-MS and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) identified 23 proteins expressed at higher levels or exclusively in FHA and 29 proteins expressed at higher levels or exclusively in U87MG cells. Three proteins, ubiquitin, cystatin B, and tissue transglutaminase (TTG), were upregulated in U87MG⌬EGFR relative to U87MG. Four proteins highly expressed by U87MG cells, Hsp27, major vault protein, TTG, and cystatin B, were analyzed by Western blot, ELISA, or RT-PCR in cell extracts and in tissue samples of glioblastoma multiforme (GBM; grade IV), low-grade astrocytomas (grades I and II), and nonmalignant brain lesions. All four proteins were highly expressed in GBM tissues compared to nonmalignant brain. These proteins may be used as diagnostic or functional (e.g., multiple drug resistance, invasiveness) markers for glioblastoma tumors. GLIA 42:194 -208, 2003.

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Section: Mass Spectral Identification Ofmentioning

confidence: 99%

Identification of differentially expressed proteins in human glioblastoma cell lines and tumors

Zhang

Tremblay

McDermid

et al. 2003

Glia

112

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“…That kind of approach is particularly relevant because, in order to study the structure-function relationships of glycoproteins, it is ANALYSIS OF MACROMOLECULES & necessary to distinguish the glycoforms present on each site. Allmaier's group has given a good example of this kind of study (Bacher et al, 2001). Those authors have described a general approach for the detailed characterization of sodium borohydride-reduced peptidoglycan fragments (syn.…”

Section: Oligosaccharides and Glycoconjugatesmentioning

confidence: 99%

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

Cristoni

Bernardi

2003

Mass Spectrometry Reviews

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I. Introduction 370 II. Techniques That Are Usually Employed in the Study of Bioorganic Macromolecules 371 A. Proteins and Peptides 371 B. Oligonucleotides 374 C. Oligosaccharides and Glycoconjugates 375 D. Various Complexes (DNA–Protein, Antigen–Antibody, Macromolecules–Metals) 377 III. Common Problems and Developments in the Analysis of Bioorganic Macromolecules by Mass Spectrometry 377 A. Ionization Source Problems and Developments 377 1. Sensitivity 377 2. Problems with Buffers 379 3. Multicharge Effect 381 B. Mass Analyzer Problems and Developments 381 1. Linear Dynamic Range 381 2. Tandem Mass Spectrometry 382 3. Sensitivity 382 4. Resolution 383 5. Mass Accuracy 383 IV. New Promising Technologies 384 A. Interfaces and Ionization Sources 384 1. Improvements in the Coupling of Liquid‐Phase Separation Systems to Mass Spectrometry 384 2. AP‐MALDI 384 3. Deprotonant Agents 385 4. Sonic Spray Ionization 388 5. APCI without Corona Discharge 391 B. Mass Analyzers 393 1. Linear Quadrupole Ion Trap 394 2. TOF Analyzers with New Detectors 395 3. Multiple Mass Analyzers 396 V. Software for Data Treatment 397 VI. Conclusions and Future Developments 399 Acknowledgments 400 References 400 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. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:369–406, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10062

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“…Furthermore, it produces larger particles compared with apoA-I or MSP1, a truncated version of apoA-I (apoA-I D1-22) (14), which may be relevant when accommodating larger membrane proteins. AFM was used to image individual E422k/DMPC NLPs under physiologically relevant buffer conditions, while IMS, a very sensitive and precise technique for measuring particle size (24), was used to determine size distributions for the entire NLP population. TEM was used as a third technique to further verify the size distribution obtained from AFM and IMS.…”

mentioning

confidence: 99%

Quantifying size distributions of nanolipoprotein particles with single-particle analysis and molecular dynamic simulations

Blanchette

Law

Benner

et al. 2008

Journal of Lipid Research

100

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Self-assembly of purified apolipoproteins and phospholipids results in the formation of nanometer-sized lipoprotein complexes, referred to as nanolipoprotein particles (NLPs). These bilayer constructs are fully soluble in aqueous environments and hold great promise as a model system to aid in solubilizing membrane proteins. Size variability in the self-assembly process has been recognized for some time, yet limited studies have been conducted to examine this phenomenon. Understanding the source of this heterogeneity may lead to methods to mitigate heterogeneity or to control NLP size, which may be important for tailoring NLPs for specific membrane proteins. Here, we have used atomic force microscopy, ion mobility spectrometry, and transmission electron microscopy to quantify NLP size distributions on the single-particle scale, specifically focusing on assemblies with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and a recombinant apolipoprotein E variant containing the N-terminal 22 kDa fragment (E422k). Four discrete sizes of E422k/DMPC NLPs were identified by all three techniques, with diameters centered at ?14.5, 19, 23.5, and 28 nm. Computer simulations suggest that these sizes are related to the structure and number of E422k lipoproteins surrounding the NLPs and particles with an odd number of lipoproteins are consistent with the double-belt model, in which at least one lipoprotein adopts a hairpin

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Negative and positive ion matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and positive ion nano‐electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various Bacillus species

Cited by 24 publications

References 75 publications

Identification of differentially expressed proteins in human glioblastoma cell lines and tumors

Identification of differentially expressed proteins in human glioblastoma cell lines and tumors

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

Quantifying size distributions of nanolipoprotein particles with single-particle analysis and molecular dynamic simulations

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