Characterization of Plant Glycoproteins: Analysis of Plant Glycopeptide Mass Spectrometry Data with plantGlycoMS, a Package in the R Statistical Computing Environment

2018 ◽  
pp. 205-220 ◽  
Author(s):  
Margaret R. Baker ◽  
Travers Ching ◽  
David L. Tabb ◽  
Qing X. Li
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Statistical Computing ◽  
Computing Environment ◽  
Plant Glycoproteins

Site-Specific N-Glycosylation Characterization of Windmill Palm Tree Peroxidase Using Novel Tools for Analysis of Plant Glycopeptide Mass Spectrometry Data

2016 ◽  
Vol 15 (6) ◽  
pp. 2026-2038 ◽  
Author(s):  
Margaret R. Baker ◽  
David L. Tabb ◽  
Travers Ching ◽  
Lisa J. Zimmerman ◽  
Ivan Y. Sakharov ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Palm Tree ◽  
Site Specific

Characterization of the human primary visual cortex and cerebellum proteomes using shotgun mass spectrometry-data-independent analyses

PROTEOMICS ◽  
2012 ◽  
Vol 12 (3) ◽  
pp. 500-504 ◽  
Author(s):  
Daniel Martins-de-Souza ◽  
Paul C. Guest ◽  
Francesca L. Guest ◽  
Corinna Bauder ◽  
Hassan Rahmoune ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Visual Cortex ◽  
Primary Visual Cortex ◽  
Mass Spectrometry Data ◽  
Shotgun Mass Spectrometry

Identification and characterization of a bioactive lantibiotic produced by Staphylococcus warneri

2009 ◽  
Vol 390 (5/6) ◽  
Author(s):  
Jørgen Petersen ◽  
Anders Boysen ◽  
Lotte Fogh ◽  
Kathrine Tabermann ◽  
Thomas Kofoed ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Bacterial Infections ◽  
Mass Spectrometry Data ◽  
Growth Media ◽  
Ionization Mass ◽  
Ionization Time ◽  
Staphylococcus Warneri ◽  
Flight Mass Spectrometry

AbstractLantibiotics are a group of potent antibacterial agents that contain unusual amino acids, such as the thioether amino acids lanthionine and methyllanthionine, and the didehydroamino acids didehydroalanine and didehydro-aminobutyric acid. Here, we report on an antibacterial lantibiotic peptide named SWLP1 (Staphylococcus warnerilantibiotic peptide 1), which is secreted fromStaphylococcus warneri(deposited with DSMZ, accession number DSM 16081). SWLP1 was purified from growth media. The purified peptide displays antibacterial activity against several species, includingStaphylococcus epidermidis. The molecular mass of SWLP1 is 2998.9 Da as determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The sequence and possible structure was elucidated by combining electrospray ionization mass spectrometry/mass spectrometry data of ethanethiol-treated and non-ethanethiol-treated tryptic fragments of the SWLP1. SWLP1 contains three thioether bridges, one didehydroalanine, and three didehydroaminobutyric acids. This peptide has the potential to be used in treatment of several Gram-positive bacterial infections.

scholarly journals Relative Quantification: Characterization of Bias, Variability and Fold Changes in Mass Spectrometry Data from iTRAQ-Labeled Peptides

2011 ◽  
Vol 10 (9) ◽  
pp. 4325-4333 ◽  
Author(s):  
Douglas W. Mahoney ◽  
Terry M. Therneau ◽  
Carrie J. Heppelmann ◽  
LeeAnn Higgins ◽  
Linda M. Benson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Relative Quantification

scholarly journals Dereplikace látek a de novo charakterizace malých molekul z hmotnostních spekter

2022 ◽  
Vol 116 (1) ◽  
pp. 11-19
Author(s):  
Jiří Novák ◽  
Vladimír Havlíček
Keyword(s):  
Mass Spectrometry ◽  
Small Molecules ◽  
Mass Spectra ◽  
De Novo ◽  
Imaging Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Liquid Chromatography Mass Spectrometry ◽  
Imaging Mass Spectrometry Data

We describe the molecular dereplication principles and de novo characterization of small molecules obtained from liquid-chromatography mass spectrometry and imaging mass spectrometry data sets. Our methodology aims at supporting chemists and computer programmers to understand the hidden computing algorithms used for metabolomics mass spectrometry data processing. The approaches have been made available in the open-source tool CycloBranch. The presented tutorial extends the interpretation of mass spectra portfolia described in a series of papers published in Chemicke Listy, issues 2/2020 and 3/2020.

scholarly journals Structural characterization of muropeptides fromChlamydia trachomatispeptidoglycan by mass spectrometry resolves “chlamydial anomaly”

2015 ◽  
Vol 112 (37) ◽  
pp. 11660-11665 ◽  
Author(s):  
Mathanraj Packiam ◽  
Brian Weinrick ◽  
William R. Jacobs ◽  
Anthony T. Maurelli
Keyword(s):  
Mass Spectrometry ◽  
Infected Cell ◽  
Mass Spectrometry Data ◽  
Ionization Mass ◽  
Cell Lysates ◽  
Susceptibility Data ◽  
Filtration Step ◽  
Double Filtration ◽  
Labeling Method

The “chlamydial anomaly,” first coined by James Moulder, describes the inability of researchers to detect or purify peptidoglycan (PG) from pathogenic Chlamydiae despite genetic and biochemical evidence and antibiotic susceptibility data that suggest its existence. We recently detected PG inChlamydia trachomatisby a new metabolic cell wall labeling method, however efforts to purify PG from pathogenic Chlamydiae have remained unsuccessful. Pathogenic chlamydial species are known to activate nucleotide-binding oligomerization domain-containing protein 2 (NOD2) innate immune receptors by as yet uncharacterized ligands, which are presumed to be PG fragments (muramyl di- and tripeptides). We used the NOD2-dependent activation of NF-κB byC. trachomatis-infected cell lysates as a biomarker for the presence of PG fragments within specific lysate fractions. We designed a new method of muropeptide isolation consisting of a double filtration step coupled with reverse-phase HPLC fractionation ofChlamydia-infected HeLa cell lysates. Fractions that displayed NOD2 activity were analyzed by electrospray ionization mass spectrometry, confirming the presence of muramyl di- and tripeptides inChlamydia-infected cell lysate fractions. Moreover, the mass spectrometry data of large muropeptide fragments provided evidence that transpeptidation and transglycosylation reactions occur in pathogenic Chlamydiae. These results reveal the composition of chlamydial PG and disprove the “glycanless peptidoglycan” hypothesis.

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