Oxidative protein labeling in mass-spectrometry-based proteomics

Roeser, Julien; Bischoff, Rainer; Bruins, Andries P.; Permentier, Hjalmar P.

doi:10.1007/s00216-010-3471-8

Cited by 41 publications

(43 citation statements)

References 180 publications

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“…Mass spectrometry alone cannot provide direct information about protein 3D structure in solution, and therefore must be used with labeling techniques such as H/D exchange [1–6], cross-linking [7–14], covalent labeling [15–17], and non-covalent labeling [18–20]. Alternatively, ion mobility mass spectrometry can also be used to study protein structure in the gas phase [21–23].…”

Section: Introductionmentioning

confidence: 99%

Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

Zhou

Vachet

2012

J. Am. Soc. Mass Spectrom.

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Covalent labeling and mass spectrometry are seeing increased used together as a way to obtain insight into the 3-dimensional structure of proteins and protein complexes. Several amino acid specific (e.g. diethylpyrocarbonate) and non-specific (e.g. hydroxyl radicals) labeling reagents are available for this purpose. Diethylpyrocarbonate (DEPC) is a promising labeling reagent because it can potentially probe up to 30% of the residues in the average protein and gives only one reaction product, thereby facilitating mass spectrometric analysis. It was recently reported, though, that DEPC modifications are labile for some amino acids. Here, we show that label loss is more significant and widespread than previously thought, especially for Ser, Thr, Tyr, and His residues, when relatively long protein digestion times are used. Such label loss ultimately decreases the amount of protein structural information that is obtainable with this reagent. We find, however, that the number of DEPC modified residues, and thus protein structural information, can be significantly increased by decreasing the time between the covalent labeling reaction and the mass spectrometric analysis. This is most effectively accomplished using short (e.g. 2 h) proteolytic digestions with enzymes such as immobilized chymotrypsin or Glu-C rather than using methods (e.g. microwave or ultrasonic irradiation) that accelerate proteolysis in other ways. Using short digestion times, we show that the percentage of solvent accessible residues that can be modified by DEPC increases from 44% to 67% for cytochrome c, 35% to 81% for myoglobin, and 76% to 95% for β-2-microglobulin. In effect, these increased numbers of modified residues improve the protein structural resolution available from this covalent labeling method. As compared to typical overnight digestion conditions, the short digestion times decrease the average distance between modified residues from 11 Å to 7 Å for myoglobin, 13 Å to 10 Å for cytochrome c, and 9 Å to 8 Å for β-2-microglobulin.

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Section: Introductionmentioning

confidence: 99%

Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

Zhou

Vachet

2012

J. Am. Soc. Mass Spectrom.

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“…Electrochemically generated modifications of proteins were reviewed by Roeser et al [50]. Electrochemical oxidation of peptides and proteins combined with mass spectrometry (MS) has revealed specific cleavage of the peptide bond at the C-terminal side of Tyr and Trp residues [51].…”

Section: Biomolecule Modificationmentioning

confidence: 99%

Hyphenation of Electrochemistry with Mass Spectrometry for Bioanalytical Studies

Cindric

Matysik

2013

Advances in Chemical Bioanalysis

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Hyphenation of electrochemistry (EC) and mass spectrometry (MS) is a growing research field with particular importance for bioanalytical applications. It opens the way for studying reaction mechanisms and metabolic pathways of biological compounds and drugs. Electrochemical conversion of sample molecules prior to MS analysis gives rise to short-lived intermediates and products naturally occurring in biological systems, which leads to better understanding of physiological processes. Numerous interesting and attractive studies in this field have been published so far demonstrating potential of EC-MS coupling. The combination with separation system such as liquid chromatography or capillary electrophoresis widens the scope of application providing additional information about compounds of interest. The combination of EC with liquid chromatography has been the most frequently used hyphenated system due to the simplicity of coupling to mass spectrometric detection. In terms of bioanalytical applications capillary electrophoresis offers some advantages and is a complementary technique to liquid chromatography. This review summarizes recent developments in this field from both instrumental and application perspectives. A rather new approach of coupling electrochemistry-capillary electrophoresis-mass spectrometry and its potential for bioanalysis is presented.

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“…65, 66 Additionally, global and site-specific glycosylation can be visualized using stains such as the Pro-Q Emerald stain. 67 Therefore, adding the posttranslational dimension to the ECM proteome catalog is quite possible.…”

Section: Future Directions and Conclusionmentioning

confidence: 99%

Using Extracellular Matrix Proteomics to Understand Left Ventricular Remodeling

Lindsey

Weintraub

Lange

2012

Circ Cardiovasc Genet

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Survival following myocardial infarction (MI) has improved substantially over the last 40 years; however, the incidence of subsequent congestive heart failure has dramatically increased as a consequence. Discovering plasma markers that signify adverse cardiac remodeling may allow high-risk patients to be recognized earlier and may provide an improved way to assess treatment efficacy. Alterations in extracellular matrix (ECM) regulate cardiac remodeling following MI and potentially provide a large array of candidate indicators. The field of cardiac proteomics has progressed rapidly over the past 20 years, since publication of the first two-dimensional electrophoretic gels of left ventricle proteins. Proteomic approaches are now routinely utilized to better understand how the left ventricle responds to injury. In this review, we will discuss how methods have developed to allow comprehensive evaluation of the ECM proteome. We will explain how ECM proteomic data can be used to predict adverse remodeling for an individual patient and highlight future directions. Although this review will focus on the use of ECM proteomics to better understand post-MI remodeling responses, these approaches have applicability to a wide-range of cardiac pathologies, including pressure overload hypertrophy, viral myocarditis, and non-ischemic heart failure.

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Oxidative protein labeling in mass-spectrometry-based proteomics

Cited by 41 publications

References 180 publications

Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

Hyphenation of Electrochemistry with Mass Spectrometry for Bioanalytical Studies

Using Extracellular Matrix Proteomics to Understand Left Ventricular Remodeling

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