scholarly journals Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Kristine K Dennis ◽  
Karan Uppal ◽  
Ken H Liu ◽  
Chunyu Ma ◽  
Bill Liang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Metal Complexes ◽  
Chain Length ◽  
High Resolution Mass Spectrometry ◽  
R Package ◽  
Large Set ◽  
Mass Spectral ◽  
And Function ◽  
Impact Absorption

Abstract Phytochelatins (PyCs) are a diverse set of plant compounds that chelate metals, protect against metal toxicity and function in metal homeostasis. PyCs are present in plants consumed as food by humans and could, in principle, impact absorption and utilization of essential and toxic metals such as selenium and cadmium, respectively. PyCs vary in terminal amino acid composition and chain length, exist in multiple oxidation states and reversibly bind multiple metals; consequently, PyCs include a large set of possible structures. Although individual PyC-metal complexes have been studied, no resource exists to characterize the diversity of PyCs and PyC-metal complexes. We used the scientific literature to develop a database of elemental formulas for polymer forms varying in chain length from 2 to 11 glutamyl-cysteine repeats. Using elemental formulas, we calculated monoisotopic masses using the most abundant isotopes of each element and calculated masses for complexes with 13 metals of nutritional and toxicological significance. The resulting phytochelatin database (PyCDB) contains 46 260 unique elemental formulas for PyC and PyC-metal complexes. The database is available online for download as well as for direct mass queries for mass spectrometry using an accurate mass annotation tool for user-selected PyC types, metals and adducts of interest. We performed studies of a commonly consumed food—onion—to validate the database and test utility of the tool. Onion samples were analyzed using ultra-high resolution mass spectrometry-based metabolomics. Mass spectral features were annotated using the PyCDB web tool and the R package, xMSannotator; annotated features were further validated by collision-induced dissociation mass spectrometry. The results establish use and a workflow for PyCDB as a resource for characterization of PyCs and PyC-metal complexes.

scholarly journals Mass Spectrometry-Based Characterization of New Spirolides from Alexandrium ostenfeldii (Dinophyceae)

Marine Drugs ◽  
2020 ◽  
Vol 18 (10) ◽  
pp. 505
Author(s):  
Joyce A. Nieva ◽  
Jan Tebben ◽  
Urban Tillmann ◽  
Sylke Wohlrab ◽  
Bernd Krock
Keyword(s):  
Mass Spectrometry ◽  
High Resolution Mass Spectrometry ◽  
Molecular Ions ◽  
Ring System ◽  
The Other ◽  
Spectral Techniques ◽  
Mass Spectral ◽  
Alexandrium Ostenfeldii ◽  
Different Strains

Spirolides belong to a group of marine phycotoxins produced by the marine planktonic dinophyte Alexandrium ostenfeldii. Composed of an imine moiety and a spiroketal ring system within a macrocylcle, spirolides are highly diverse with toxin types that vary among different strains. This study aims to characterize the spirolides from clonal A. ostenfeldii strains collected from The Netherlands, Greenland and Norway by mass spectral techniques. The structural characterization of unknown spirolides as inferred from high-resolution mass spectrometry (HR-MS) and collision induced dissociation (CID) spectra revealed the presence of nine novel spirolides that have the pseudo-molecular ions m/z 670 (1), m/z 666 (2), m/z 696 (3), m/z 678 (4), m/z 694 (5), m/z 708 (6), m/z 720 (7), m/z 722 (8) and m/z 738 (9). Of the nine new spirolides proposed in this study, compound 1 was suggested to have a truncated side chain in lieu of the commonly observed butenolide ring in spirolides. Moreover, there is indication that compound 5 might belong to new spirolide subclasses with a trispiroketal ring configuration having a 6:5:6 trispiroketal ring system. On the other hand, the other compounds were proposed as C- and G-type SPX, respectively. Compound 7 is proposed as the first G-type SPX with a 10-hydroxylation as usually observed in C-type SPX. This mass spectrometry-based study thus demonstrates that structural variability of spirolides is larger than previously known and does not only include the presence or absence of certain functional groups but also involves the triketal ring system.

A Mucin-Specific Protease Enables Molecular and Functional Analysis of Human Cancer-Associated Mucins

2018 ◽  
Author(s):  
Stacy A. Malaker ◽  
Kayvon Pedram ◽  
Michael J. Ferracane ◽  
Elliot C. Woods ◽  
Jessica Kramer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Mechanisms ◽  
Cultured Cells ◽  
High Resolution Mass Spectrometry ◽  
Human Cancer ◽  
Glycosylation Sites ◽  
Bacterial Protease ◽  
Specific Protease ◽  
To Come ◽  
And Function

<div> <div> <div> <p>Mucins are a class of highly O-glycosylated proteins that are ubiquitously expressed on cellular surfaces and are important for human health, especially in the context of carcinomas. However, the molecular mechanisms by which aberrant mucin structures lead to tumor progression and immune evasion have been slow to come to light, in part because methods for selective mucin degradation are lacking. Here we employ high resolution mass spectrometry, polymer synthesis, and computational peptide docking to demonstrate that a bacterial protease, called StcE, cleaves mucin domains by recognizing a discrete peptide-, glycan-, and secondary structure- based motif. We exploited StcE’s unique properties to map glycosylation sites and structures of purified and recombinant human mucins by mass spectrometry. As well, we found that StcE will digest cancer-associated mucins from cultured cells and from ovarian cancer patient-derived ascites fluid. Finally, using StcE we discovered that Siglec-7, a glyco-immune checkpoint receptor, specifically binds sialomucins as biological ligands, whereas the related Siglec-9 receptor does not. Mucin-specific proteolysis, as exemplified by StcE, is therefore a powerful tool for the study of glycoprotein structure and function and for deorphanizing mucin-binding receptors. </p> </div> </div> </div>

scholarly journals A combined flow injection/reversed phase chromatography – high resolution mass spectrometry workflow for accurate absolute lipid quantification with 13C- internal standards

The Analyst ◽  
2021 ◽  
Author(s):  
Harald Schoeny ◽  
Evelyn Rampler ◽  
Yasin El Abiead ◽  
Felina Hildebrand ◽  
Olivia Zach ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Flow Injection ◽  
High Resolution Mass Spectrometry ◽  
Reversed Phase ◽  
Internal Standards ◽  
Lipid Quantification ◽  
High Resolution Mass ◽  
Resolution Mass

We propose a fully automated novel workflow for lipidomics based on flow injection- followed by liquid chromatography high resolution mass spectrometry (FI/LC-HRMS). The workflow combined in-depth characterization of the lipidome...

Structural Characterization of Complex Bacterial Glycolipids by Fourier Transform Mass Spectrometry

2005 ◽  
Vol 11 (5) ◽  
pp. 535-546 ◽  
Author(s):  
Anna Kondakov ◽  
Buko Lindner
Keyword(s):  
Mass Spectrometry ◽  
Fourier Transform ◽  
Structural Information ◽  
Adaptive Immune System ◽  
Ion Cyclotron Resonance ◽  
Bacterial Membranes ◽  
Multiphoton Dissociation ◽  
The One ◽  
And Function

Bacterial glycolipids are complex amphiphilic molecules which are, on the one hand, of utmost importance for the organization and function of bacterial membranes and which, on the other hand, play a major role in the activation of cells of the innate and adaptive immune system of the host. Already small alterations to their chemical structure may influence the biological activity tremendously. Due to their intrinsic biological heterogeneity [number and type of fatty acids, saccharide structures and substitution with for example, phosphate ( P), 2-aminoethyl-(pyro)phosphate groups ( P-Etn) or 4-amino-4-deoxyarabinose (Ara4N)], separation of the different components are a prerequisite for unequivocal chemical and nuclear magnetic resonance structural analyses. In this contribution, the structural information which can be obtained from heterogenous samples of glycolipids by Fourier transform (FT) ion cyclotron resonance mass spectrometric methods is described. By means of recently analysed complex biological samples, the possibilities of high-resolution electrospray ionization FT-MS are demonstrated. Capillary skimmer dissociation, as well as tandem mass spectrometry (MS/MS) analysis utilizing collision-induced dissociation and infrared multiphoton dissociation, are compared and their advantages in providing structural information of diagnostic importance are discussed.

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