Challenges in mass spectrometry‐based proteomics

Reinders, Joerg; Lewandrowski, Urs; Moebius, Jan; Wagner, Yvonne; Sickmann, Albert

doi:10.1002/pmic.200400869

Cited by 157 publications

(111 citation statements)

References 110 publications

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“…During the last few years, the proteomic approach has been established as a powerful tool for analyzing various biological phenomena [20]. In general, the amount of mRNA and proteins are not always correlated with each other because of the posttranscriptional mechanisms controlling translational rates, half-lives, and PTM of proteins [21,22].…”

Section: Introductionmentioning

confidence: 99%

Circadian proteomics of the mouse retina

et al. 2007

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The circadian clock in the retina regulates a variety of physiological phenomena such as disc shedding and melatonin release. Although these events are critical for retinal functions, it is almost unknown how the circadian clock controls the physiological rhythmicity. To gain insight into the processes, we performed a proteomic analysis using 2-DE to find proteins whose levels show circadian changes. Among 415 retinal protein spots, 11 protein spots showed circadian rhythmicity in their intensities. We performed MALDI-TOF MS and NanoLC-MS/MS analyses and identified proteins contained in the 11 spots. The proteins were related to vesicular transport, calcium-binding, protein degradation, metabolism, RNA-binding, and protein foldings, suggesting the clock-regulation of neurotransmitter release, transportation of the membrane proteins, calcium-binding capability, and so on. We also found a rhythmic phosphorylation of N-ethylmaleimide-sensitive fusion protein and identified one of the amino acid residues modified by phosphorylation. These findings provide a new perspective on the relationship between the physiological functions of the retina and the circadian clock system.

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Section: Introductionmentioning

confidence: 99%

Circadian proteomics of the mouse retina

et al. 2007

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“…While protein analysis have been established as new tools for understanding various biological problems, different mass spectrometric techniques for identification and posttranslational modifications have been established as well as isolation and separation methods for analysis of highly complex samples by classical separation techniques, such as two-dimensional gel electrophoresis and liquid chromatography (Lescuyer et al, 2004;Reinders et al, 2004). Recently, these techniques have been helpful for macrophage proteome analysis (Walsh et al, 1995;Yeung and Stanley, 2003;Yu et al, 2003;Verhoeckx et al, 2004;Dupont et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

Proteomic fingerprints distinguish microglia, bone marrow, and spleen macrophage populations

Enose

Destache

Mack

et al. 2005

Glia

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Mononuclear phagocytes (MP; dendritic cells, monocytes, tissue macrophages, and microglia) maintain tissue homeostasis and provide a first line of defense against invading pathogens. In specific circumstances, MPs also induce inflammatory responses and as such affect disease onset and progression. Despite intensive research into MP biology, little is known of the functional and molecular properties of individual MP subtypes. Using a novel proteomics platform, unique protein patterns and protein identities were observed among populations of spleen and bone marrow macrophages and microglia. Cells were obtained from C57BL/6 mice and were cultivated in macrophage colony‐stimulating factor. MP subtypes were indistinguishable by morphological or antigenic criteria. Protein profiling by Surface Enhanced Laser Desorption Ionization‐Time of Flight (SELDI‐TOF) ProteinChip® assays with weak cationic exchange chips showed unique MP spectral profiles. Corresponding protein fractions were recovered by high performance liquid chromatography and identified by liquid chromatography tandem mass spectrometry. The results provide a unique means to distinguish microglia from other MP subtypes. © 2005 Wiley‐Liss, Inc.

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“…In addition, such an approach enables to reveal proteins that were not detected as distinct spots by 2-DE analysis. Usage of nanochromatographic columns in a combination with the nanoelectrospray ion source of MS (LC-MS) allows for the identification of nanoamounts of proteins, reduces the solvent flow rate to a few nanolitre per minute and consequently ensures an over 100-fold increase in sensitivity compared to common chromatography -at the cost of the system's minimization [28]. The concentration limit -upon application of electrophoresis or chromatography in a combination with MS -is determined by the electrophoretic or chromatographic stages since the sensitivity of mass-spectrometric analysis may reach the attomolar levels -as was demonstrated in experiments with bradykinin and cytochrome C [29].…”

Section: Nanoelectrophoresis Nanochromatography and Magnetic Biobeadmentioning

confidence: 99%

Nanotechnologies in proteomics

Ivanov

Govorun

Быков³

et al. 2006

Proteomics

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Progress in proteomic researches is largely determined by development and implementation of new methods for the revelation and identification of proteins in biological material in a wide concentration range (from 10 23 M to single molecules). The most perspective approaches to address this problem involve (i) nanotechnological physicochemical procedures for the separation of multicomponent protein mixtures; among these of particular interest are biospecific nanotechnological procedures for selection of proteins from multicomponent protein mixtures with their subsequent concentration on solid support; (ii) identification and counting of single molecules by use of molecular detectors. The prototypes of biospecific nanotechnological procedures, based on the capture of ligand biomolecules by biomolecules of immobilized ligate and the concentration of the captured ligands on appropriate surfaces, are well known; these are affinity chromatography, magnetic biobeads technology, different biosensor methods, etc. Here, we review the most promising nanotechnological approaches for selection of proteins and kinetic characterization of their complexes based on these biospecific methods with subsequent MS/MS identification of proteins and protein complexes. Two major groups of methods for the analysis and identification of individual molecules and their complexes by use of molecular detectors will be reviewed: scanning probe microscopy (SPM) (including atomic-force microscopy) and cryomassdetector technology.

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Challenges in mass spectrometry‐based proteomics

Cited by 157 publications

References 110 publications

Circadian proteomics of the mouse retina

Circadian proteomics of the mouse retina

Proteomic fingerprints distinguish microglia, bone marrow, and spleen macrophage populations

Nanotechnologies in proteomics

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