scholarly journals Fast photochemical oxidation of proteins (FPOP): A powerful mass spectrometry–based structural proteomics tool

2019 ◽  
Vol 294 (32) ◽  
pp. 11969-11979 ◽  
Author(s):  
Danté T. Johnson ◽  
Luciano H. Di Stefano ◽  
Lisa M. Jones
Keyword(s):  
Mass Spectrometry ◽  
Photochemical Oxidation ◽  
Structural Proteomics ◽  
Proteomics Tool

scholarly journals Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies

Biomolecules ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 135
Author(s):  
Yanchun Lin ◽  
Michael L. Gross
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Metal Binding ◽  
Metal Ion ◽  
Photochemical Oxidation ◽  
Structural Proteomics ◽  
Binding Studies ◽  
Ligand Interactions ◽  
Amino Acid Labeling

Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), “fast photochemical oxidation of proteins” (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including “protein–ligand interactions by mass spectrometry, titration and HD exchange” (PLIMSTEX) and “ligand titration, fast photochemical oxidation of proteins and mass spectrometry” (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.

scholarly journals Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Liuqing Shi ◽  
Michael L. Gross
Keyword(s):  
Mass Spectrometry ◽  
Hydroxyl Radical ◽  
Protein Modification ◽  
Solvent Accessibility ◽  
Conformational Dynamics ◽  
Photochemical Oxidation ◽  
Structural Proteomics ◽  
Sequence Coverage ◽  
Protein Footprinting

Background: Determination of the composition and some structural features of macromolecules can be achieved by using structural proteomics approaches coupled with mass spectrometry (MS). One approach is hydroxyl radical protein footprinting whereby amino-acid side chains are modified with reactive reagents to modify irreversibly a protein side chain. The outcomes, when deciphered with mass-spectrometry-based proteomics, can increase our knowledge of structure, assembly, and conformational dynamics of macromolecules in solution. Generating the hydroxyl radicals by laser irradiation, Hambly and Gross developed the approach of Fast Photochemical Oxidation of Proteins (FPOP), which labels proteins on the sub millisecond time scale and provides, with MS analysis, deeper understanding of protein structure and protein-ligand and protein- protein interactions. This review highlights the fundamentals of FPOP and provides descriptions of hydroxyl-radical and other radical and carbene generation, of the hydroxyl labeling of proteins, and of determination of protein modification sites. We also summarize some recent applications of FPOP coupled with MS in protein footprinting. Conclusion: We survey results that show the capability of FPOP for qualitatively measuring protein solvent accessibility on the residue level. To make these approaches more valuable, we describe recent method developments that increase FPOP’s quantitative capacity and increase the spatial protein sequence coverage. To improve FPOP further, several new labeling reagents including carbenes and other radicals have been developed. These growing improvements will allow oxidative- footprinting methods coupled with MS to play an increasingly significant role in determining the structure and dynamics of macromolecules and their assemblies.

scholarly journals Urban organic aerosol composition in Eastern China differs from North to South: Molecular insight from a liquid chromatography-Orbitrap mass spectrometry study

2019 ◽  
Author(s):  
Kai Wang ◽  
Ru-Jin Huang ◽  
Martin Brüggemann ◽  
Yun Zhang ◽  
Lu Yang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Eastern China ◽  
Organic Aerosol ◽  
Photochemical Oxidation ◽  
Lower Latitude ◽  
Molecular Formula ◽  
Aerosol Composition ◽  
Orbitrap Mass Spectrometry ◽  
Low Degrees

Abstract. Particulate air pollution in China is influencing human health, ecosystem and climate. However, the chemical composition of particulate aerosol, especially of the organic fraction, is still not well understood. In this study, particulate aerosol samples with a diameter ≤ 2.5 μm (PM2.5) were collected in January 2014 in three cities located in Northeast, East and Southeast China, i.e., Changchun, Shanghai and Guangzhou, respectively. Organic aerosol (OA) in the PM2.5 samples was analyzed by ultrahigh performance liquid chromatography (UHPLC) coupled to high-resolution Orbitrap mass spectrometry in both negative mode (ESI−) and positive mode electrospray ionization (ESI+). After a non-target screening including molecular formula assignments, compounds were classified into five groups based on their elemental composition, i.e., CHO, CHON, CHN, CHOS and CHONS. The CHO, CHON and CHN compounds present the dominant signal abundances of 81–99.7 % in the mass spectra and the majority of these compounds were assigned to mono- and polyaromatics, suggesting that anthropogenic emissions are a large source of urban OA in all three cities. However, the chemical characteristics of these compounds varied among different cities. The degree of aromaticity and the number of polyaromatic compounds were significantly higher in samples from Changchun, which could be attributed to the large emissions from residential heating (i.e., coal combustion) during winter time in Northeast China. Moreover, the ESI− analysis showed higher H / C and O / C ratios for organic compounds in Shanghai and Guangzhou compared to samples from Changchun, indicating that OA in lower latitude regions of China experiences more intense photochemical oxidation processes. The majority of sulfur-containing compounds (CHOS and CHONS) in all cities were assigned to aliphatic compounds with low degrees of unsaturation and aromaticity. Again, samples from Shanghai and Guangzhou exhibit a larger chemical similarity but largely differ from those from Changchun.

scholarly journals Methodology for Studying Oxidation of Organic Species in Solution

2000 ◽  
Vol 83 (3) ◽  
pp. 584-587 ◽  
Author(s):  
Susan M Grimes ◽  
Helen C Ngwang
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Inorganic Carbon ◽  
Photochemical Oxidation ◽  
Photocatalytic Decomposition ◽  
Gas Chromatography Mass Spectrometry ◽  
Uv Spectrophotometry ◽  
Total Inorganic Carbon ◽  
Organic Species ◽  
Wide Range

Abstract A photoreactor was developed to study products of photochemical oxidation in a wide range of organic compounds. Analysis of the products from the reactor were used to determine the extent of mineralization of the organic material, to characterize any intermediate compounds formed, and to obtain information on the decomposition mechanism. Appropriate methods for separation and characterization include LC, UV spectrophotometry, gas chromatography/mass spectrometry, total organic carbon, and total inorganic carbon. The uses of the reactor are described for the photocatalytic decomposition of phenol and of its major decomposition intermediates 1,2- and 1,4-dihydroxybenzene.

OXYGEN-18 TRACER EVIDENCE FOR THE TERMINATION MECHANISM IN THE PHOTOCHEMICAL OXIDATION OF ACETALDEHYDE

1963 ◽  
Vol 41 (2) ◽  
pp. 300-307 ◽  
Author(s):  
C. A. McDowell ◽  
S. Sifniades
Keyword(s):  
Mass Spectrometry ◽  
Oxygen Atom ◽  
Gas Phase ◽  
Molecular Oxygen ◽  
Photochemical Oxidation ◽  
Isotopic Ratios ◽  
Careful Study ◽  
Elimination Process

The chain-terminating step in the photochemical oxidation of acetaldehyde in the gas phase has earlier been established to be the reaction[Formula: see text]Using oxygen-18 of 99.4% purity in the form of molecular oxygen we have made a careful study of the variation of the isotopic ratios of the various oxygens, by mass spectrometry, during the course of the photooxidation. The results show conclusively that the mechanism of the termination step is:[Formula: see text]where O* represents O18. Thus the recombination terminating reaction takes place with the elimination of one oxygen atom from each reacting peroxy AcOO radical. The mechanism of this elimination process is thought to be as follows:[Formula: see text]

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