scholarly journals Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3

2021 ◽  
Author(s):  
Wen-Feng Zeng ◽  
Wei-Qian Cao ◽  
Ming-Qi Liu ◽  
Si-Min He ◽  
Peng-Yuan Yang
Keyword(s):  
Data Interpretation ◽  
Comprehensive Analysis ◽  
Accurate Identification ◽  
Flexible Tool ◽  
Specific Level ◽  
Site Specific ◽  
Mass Spectrometric Data ◽  
Spectrometric Data ◽  
Fast Speed ◽  
Made In

AbstractGreat advances have been made in mass spectrometric data interpretation for intact glycopeptide analysis. However, accurate identification of intact glycopeptides and modified saccharide units at the site-specific level and with fast speed remains challenging. Here, we present a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units. A glycan ion-indexing algorithm developed for glycan-first search makes pGlyco3 5–40 times faster than other glycoproteomic search engines without decreasing accuracy or sensitivity. By combining electron-based dissociation spectra, pGlyco3 integrates a dynamic programming-based algorithm termed pGlycoSite for site-specific glycan localization. Our evaluation shows that the site-specific glycan localization probabilities estimated by pGlycoSite are suitable to localize site-specific glycans. With pGlyco3, we confidently identified N-glycopeptides and O-mannose glycopeptides that were extensively modified by ammonia adducts in yeast samples. The freely available pGlyco3 is an accurate and flexible tool that can be used to identify glycopeptides and modified saccharide units.

Anacyclamide D8P, a prenylated cyanobactin from a Sphaerospermopsis sp. cyanobacterium

2017 ◽  
Author(s):  
Joana Martins ◽  
Niina Leikoski ◽  
Matti Wahlsten ◽  
Joana Azevedo ◽  
Jorge Antunes ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Cyclic Peptides ◽  
Biosynthetic Gene Cluster ◽  
The Novel ◽  
Tyrosine Residue ◽  
Biosynthetic Gene ◽  
Post Translational Modification ◽  
Biological Assays ◽  
Mass Spectrometric Data ◽  
Spectrometric Data

Cyanobactins are a family of linear and cyclic peptides produced through the post-translational modification of short precursor peptides. Anacyclamides are macrocyclic cyanobactins with a highly diverse sequence that are common in the genus <i>Anabaena</i>. A mass spectrometry-based screening of potential cyanobactin producers led to the discovery of a new prenylated member of this family of compounds, anacyclamide D8P (<b>1</b>), from <i>Sphaerospermopsis</i> sp. LEGE 00249. The anacyclamide biosynthetic gene cluster (<i>acy</i>) encoding the novel macrocyclic prenylated cyanobactin, was sequenced. Heterologous expression of the acy gene cluster in <i>Escherichia</i> <i>coli</i> established the connection between genomic and mass spectrometric data. Unambiguous establishment of the type and site of prenylation required the full structural elucidation of <b>1</b> using Nuclear Magnetic Resonance (NMR), which demonstrated that a forward prenylation occurred on the tyrosine residue. Compound <b>1</b> was tested in pharmacologically or ecologically relevant biological assays and revealed moderate antimicrobial activity towards the fouling bacterium <i>Halomonas aquamarina</i> CECT 5000.<br>

Application of Factor Analysis in Imaging Mass Spectrometric Data Analysis

2014 ◽  
Vol 42 (8) ◽  
pp. 1099-1103 ◽  
Author(s):  
Yi CHEN ◽  
Fei TANG ◽  
Tie-Gang LI ◽  
Jiu-Ming HE ◽  
Zeper ABLIZ ◽  
...  
Keyword(s):  
Factor Analysis ◽  
Data Analysis ◽  
Mass Spectrometric ◽  
Mass Spectrometric Data ◽  
Spectrometric Data

Comprehensive Analysis of the Geological and Geophysical Data in the Study of the Upper Miocene Turbidite Systems of the Nam Con Son Basin, Vietnam

2021 ◽  
Author(s):  
Mariia Kurianova ◽  
Ekaterina Birkle ◽  
Tatiana Egorkina ◽  
Sergey Koltsov
Keyword(s):  
Data Interpretation ◽  
Comprehensive Analysis ◽  
Geophysical Data ◽  
Saint Petersburg ◽  
Upper Miocene ◽  
Branch Office ◽  
Sand Bodies

Abstract The article considers the approaches to the G&G data interpretation used in the Branch Office of Gazprom International in Saint Petersburg (hereinafter referred to as "GPEPI") when studying the geology aspects of turbidite deposits. This approach is showcased on one of the Upper Miocene deposits of the Nam Con Son Basin in Vietnam, and a conclusion is drawn about the possibility of using this complex technique in the study of sand bodies of any genesis.

scholarly journals Speech After Long Silence—An Appraisee-Based Comprehensive Analysis With Retrospective and Future Perspectives on Current ID Policy of Transpersons in China

2021 ◽  
Vol 9 ◽  
Author(s):  
Jian Shi ◽  
Yadong Guo ◽  
María José Cavagnaro ◽  
Jifeng Cai ◽  
Zhuoying Liu
Keyword(s):  
Comprehensive Analysis ◽  
Sex Reassignment Surgery ◽  
Sex Reassignment ◽  
Future Perspectives ◽  
Significant Progress ◽  
Police Station ◽  
Local Police ◽  
Developmental Conditions ◽  
Male To Female ◽  
Made In

As the sexual minority in China, transpersons remain faced with various realistic challenges. In recent years, however, there has been a significant progress made in the protection given to the rights that transpersons deserve. Currently, the citizens who have changed their gender through sex reassignment surgery can make applications to the local police station for changing their gender registration and get issued a new ID card. This is regarded as a crucial milestone in reducing the bias against transpersons and protecting their legitimate rights in China. Highlighted by the case of an extraordinary appraisee who have received SRS to change from male to female and started a new life with a new ID, not only does this article construe the current ID policy and the detailed process of ID card change for transpersons in China, it also reveals the living and developmental conditions facing transpersons in China. Finally, the visibility of the community of transpersons is improved to eradicate the discrimination against transpersons.

scholarly journals Four Portraits, No Retouching

2020 ◽  
Vol 7 (3) ◽  
pp. 97-113
Author(s):  
Pavel Fokin
Keyword(s):  
Russian Literature ◽  
Comprehensive Analysis ◽  
Comprehensive Examination ◽  
State Museum ◽  
History Of ◽  
Made In

Researchers are still raising questions related to the time and place of shooting of certain portraits in the scarce photographic iconography of F. M. Dostoevsky. First of all, this pertains to a set of early photographs, whose dating ranges between 1857 and 1863, according to various sources. The article offers new arguments in favor of attributing several portraits of F. M. Dostoevsky to 1859. This refers to photographs that captured an image of F. M. Dostoevsky that is unusual for most of his admirers, namely, without a beard. Two of them were taken in Semipalatinsk by the photographer S. A. Leibin, while in one of them F. M. Dostoevsky was captured together with the Kazakh educator Ch. Ch. Valikhanov, whom he befriended during the years of his exile. Another photo has not been precisely attributed. A comprehensive analysis of the details depicted on them, the facts of the biography of Ch. Ch. Valikhanov and the letters of F. M. Dostoevsky allows to date the Semipalatisk photographs with greater accuracy. The article proposes that another one of the portraits taken in Tver was carried out simultaneously with the shooting of the portrait of M. M. Dostoevsky. A comprehensive examination of various details and circumstances also leads to the same conclusions. To date, only a few copies of photographs with Ch. Ch. Valikhanov and a photograph allegedly taken in Tver are known. The original solitary portrait made in Semipalatinsk has been lost. The conducted research allows to assert that other copies of these photographs may exist. The proposed conclusions are made on the basis of a study of the originals of photographs in the collection of The V. I. Dahl State Museum of the History of Russian Literature.

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