scholarly journals Improved method for the analysis of membrane proteins by mass spectrometry

2007 ◽  
Vol 30 (1) ◽  
pp. 89-94 ◽  
Author(s):  
Shama P. Mirza ◽  
Brian D. Halligan ◽  
Andrew S. Greene ◽  
Michael Olivier
Keyword(s):  
Mass Spectrometry ◽  
Membrane Proteins ◽  
Peptide Ions ◽  
Membrane Bilayer ◽  
Mass Spectral ◽  
Associated Proteins ◽  
Mass Spectrometric Identification ◽  
Membrane Bound ◽  
Positively Charged

Membrane-bound and membrane-associated proteins are difficult to analyze by mass spectrometry, since the association with lipids impedes the isolation and solubilization of the proteins in buffers suitable for mass spectrometry and the efficient generation of positively charged peptide ions by electrospray ionization. Current methods mostly utilize detergents for the isolation of proteins from membranes. In this study, we present an improved detergent-free method for the isolation and mass spectrometric identification of membrane-bound and membrane-associated proteins. We delipidate proteins from the membrane bilayer by chloroform extraction to overcome dissolution and ionization problems during analysis. Comparison of our results to results obtained by direct tryptic digestion of insoluble membrane pellets identifies an increased number of membrane proteins, and a higher quality of the resulting mass spectral data.

Enhancing the mass spectrometric identification of membrane proteins by combining chemical and enzymatic digestion methods

2015 ◽  
Vol 7 (17) ◽  
pp. 7220-7227 ◽  
Author(s):  
Johanna M. Smeekens ◽  
Weixuan Chen ◽  
Ronghu Wu
Keyword(s):  
Mass Spectrometry ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Analysis ◽  
Enzymatic Digestion ◽  
Mass Spectrometric ◽  
Spectrometric Identification ◽  
Mass Spectrometric Identification ◽  
Digestion Methods

Combining chemical and enzymatic digestion methods proved to be extremely effective for mass-spectrometry (MS)-based membrane protein analysis.

scholarly journals Identification of Novel Antigenic Proteins in a Complex Anaplasma marginale Outer Membrane Immunogen by Mass Spectrometry and Genomic Mapping

2005 ◽  
Vol 73 (12) ◽  
pp. 8109-8118 ◽  
Author(s):  
Job E. Lopez ◽  
William F. Siems ◽  
Guy H. Palmer ◽  
Kelly A. Brayton ◽  
Travis C. McGuire ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Vaccine Development ◽  
Outer Membrane Proteins ◽  
Serum Antibody ◽  
Elongation Factor ◽  
Anaplasma Marginale ◽  
Antigenic Proteins ◽  
Associated Proteins

ABSTRACT Immunization with purified Anaplasma marginale outer membranes induces complete protection against infection that is associated with CD4+ T-lymphocyte-mediated gamma interferon secretion and immunoglobulin G2 (IgG2) antibody titers. However, knowledge of the composition of the outer membrane immunogen is limited. Recent sequencing and annotation of the A. marginale genome predicts at least 62 outer membrane proteins (OMP), enabling a proteomic and genomic approach for identification of novel OMP by use of IgG serum antibody from outer membrane vaccinates. Outer membrane proteins were separated by two-dimensional electrophoresis, and proteins recognized by total IgG and IgG2 in immune sera of outer membrane-vaccinated cattle were detected by immunoblotting. Immunoreactive protein spots were excised and subjected to liquid chromatography-tandem mass spectrometry. A database search of the A. marginale genome identified 24 antigenic proteins that were predicted to be outer membrane, inner membrane, or membrane-associated proteins. These included the previously characterized surface-exposed outer membrane proteins MSP2, operon associated gene 2 (OpAG2), MSP3, and MSP5 as well as recently identified appendage-associated proteins. Among the 21 newly described antigenic proteins, 14 are annotated in the A. marginale genome and include type IV secretion system proteins, elongation factor Tu, and members of the MSP2 superfamily. The identification of these novel antigenic proteins markedly expands current understanding of the composition of the protective immunogen and provides new candidates for vaccine development.

scholarly journals Curatr: a web application for creating, curating, and sharing a mass spectral library

2017 ◽  
Author(s):  
Andrew Palmer ◽  
Prasad Phapale ◽  
Dominik Fay ◽  
Theodore Alexandrov
Keyword(s):  
Mass Spectrometry ◽  
Web Application ◽  
Mass Spectrometry Analysis ◽  
Supplementary Information ◽  
Spectral Library ◽  
Mass Spectral Fragmentation ◽  
Mass Spectral ◽  
Link Type ◽  
Manual Curation

AbstractMotivationIdentification from metabolomics mass spectrometry experiments requires comparison of fragmentation spectra from experimental samples to spectra from analytical standards. As the quality of identification depends directly on the quality of the reference spectra, manual curation is routine during the selection of reference spectra to include in a spectral library. Whilst building our own in-house spectral library we realised that there is currently no vendor neutral open access tool for for facilitating manual curation of spectra from raw LC-MS data into a custom spectral library.ResultsWe developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries for liquid-chromatography mass spectrometry analysis. Curatr handles datasets from single or multiplexed standards, automatically extracting chromatographic profiles and potential fragmentation spectra for multiple adducts. These are presented through an intuitive interface for manual curation before being documented in a custom spectral library. Searchable molecular information and the providence of each standard is stored along with metadata on the experimental protocol. Curatr support the export of spectral libraries in several standard formats for easy use with third party software or submission to community databases, maximising the return on investment for these costly measurements. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library which is publicly available at http://curatr.mcf.embl.de.AvailabilityThe source code is freely available at http://github.com/alexandrovteam/curatr/ along with example data.Supplementary informationA step-by step user manual is available in the supplementary information

scholarly journals Glycan-protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces

2021 ◽  
Author(s):  
Yixuan Xie ◽  
Siyu Chen ◽  
Qiongyu Li ◽  
Ying Sheng ◽  
Michael R Alvarez ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sialic Acid ◽  
Membrane Proteins ◽  
Cell Membranes ◽  
Sialic Acids ◽  
Cross Linking ◽  
Protein Networks ◽  
Cell Surfaces ◽  
Protein Cross Linking

A cross-linking method is developed to elucidate the glycan-mediated interactions between membrane proteins through sialic acids. The method provides previously unknown extensive glycomic interactions on cell membranes. The vast majority...

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