22,637 research outputs found
Clickable report tags for identification of modified peptides by mass spectrometry
The identification and quantification of modified peptides are critical for the functional characterization of post-translational protein modifications (PTMs) to elucidate their biological function. Nowadays, quantitative mass spectrometry coupled with various bioinformatic pipelines has been successfully used for the determination of a wide range of PTMs. However, direct characterization of low abundant protein PTMs in bottom-up proteomic workflow remains challenging. Here, we present the synthesis and evaluation of tandem mass spectrometry tags (TMT) which are introduced via click-chemistry into peptides bearing alkyne handles. The fragmentation properties of the two mass tags were validated and used for screening in a model system and analysis of AMPylated proteins. The presented tags provide a valuable tool for diagnostic peak generation to increase confidence in the identification of modified peptides and potentially for direct peptide-PTM quantification from various experimental conditions
Mass Spectrometry in the Elucidation of the Glycoproteome of Bacterial Pathogens
Presently some three hundred post-translational modifications are known to occur in bacteria in vivo. Many of
these modifications play critical roles in the regulation of proteins and control key biological processes. One of the most
predominant modifications, N- and O-glycosylations are now known to be present in bacteria (and archaea) although they
were long believed to be limited to eukaryotes. In a number of human pathogens these glycans have been found attached
to the surfaces of pilin, flagellin and other surface and secreted proteins where it has been demonstrated that they play a
role in the virulence of these bacteria. Mass spectrometry characterization of these glycosylation events has been the enabling
key technology for these findings. This review will look at the use of mass spectrometry as a key technology for the
detection and mapping of these modifications within microorganisms, with particular reference to the human pathogens,
Campylobacter jejuni and Mycobacterium tuberculosis. The overall aim of this review will be to give a basic understanding
of the current ‘state-of-the-art’ of the key techniques, principles and technologies, including bioinformatics tools, involved
in the analysis of the glycosylation modifications
Protein Sequencing with an Adaptive Genetic Algorithm from Tandem Mass Spectrometry
In Proteomics, only the de novo peptide sequencing approach allows a partial
amino acid sequence of a peptide to be found from a MS/MS spectrum. In this
article a preliminary work is presented to discover a complete protein sequence
from spectral data (MS and MS/MS spectra). For the moment, our approach only
uses MS spectra. A Genetic Algorithm (GA) has been designed with a new
evaluation function which works directly with a complete MS spectrum as input
and not with a mass list like the other methods using this kind of data. Thus
the mono isotopic peak extraction step which needs a human intervention is
deleted. The goal of this approach is to discover the sequence of unknown
proteins and to allow a better understanding of the differences between
experimental proteins and proteins from databases
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A mass spectrometry-guided genome mining approach for natural product peptidogenomics.
Peptide natural products show broad biological properties and are commonly produced by orthogonal ribosomal and nonribosomal pathways in prokaryotes and eukaryotes. To harvest this large and diverse resource of bioactive molecules, we introduce here natural product peptidogenomics (NPP), a new MS-guided genome-mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters by iteratively matching de novo tandem MS (MS(n)) structures to genomics-based structures following biosynthetic logic. In this study, we show that NPP enabled the rapid characterization of over ten chemically diverse ribosomal and nonribosomal peptide natural products of previously unidentified composition from Streptomycete bacteria as a proof of concept to begin automating the genome-mining process. We show the identification of lantipeptides, lasso peptides, linardins, formylated peptides and lipopeptides, many of which are from well-characterized model Streptomycetes, highlighting the power of NPP in the discovery of new peptide natural products from even intensely studied organisms
Power and limitations of electrophoretic separations in proteomics strategies
Proteomics can be defined as the large-scale analysis of proteins. Due to the
complexity of biological systems, it is required to concatenate various
separation techniques prior to mass spectrometry. These techniques, dealing
with proteins or peptides, can rely on chromatography or electrophoresis. In
this review, the electrophoretic techniques are under scrutiny. Their
principles are recalled, and their applications for peptide and protein
separations are presented and critically discussed. In addition, the features
that are specific to gel electrophoresis and that interplay with mass
spectrometry (i.e., protein detection after electrophoresis, and the process
leading from a gel piece to a solution of peptides) are also discussed
Beyond DNA: Epigenetics and Proteomics in Forensic Science
The use of genetic evidence in criminal cases is well established and has improved the public opinion and credibility of forensic science. However, several shortcomings associated with current genetic profiling techniques exist. Scientific research aimed at increasing the overall knowledge and understanding of biological factors will lead to the development of methods capable of improving the discriminating power of DNA evidence, overcoming limitations associated with DNA evidence, or complementing current methods of DNA profiling. Increased research in the fields of epigenetics and proteomics are particularly promising and relevant to forensic science. Research suggests that epigenetic biomarkers can be used to approximate the age of biological sample donors, differentiate between DNA of monozygotic twins, distinguish between natural and synthesized DNA, and identify body fluid sources from forensic material. Proteomic research studies indicate that mass spectrometry can be used to identify biological matrices and tissue sources from forensic biological samples without compromising DNA evidence. The demand for improved forensic techniques necessitates further research into these fields and, specifically, how the associated methods can be used in forensic science
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