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Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

Methods and Algorithms for Quantitative Proteomics by Mass S...

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作者： Rune Matthiesen Ana Sofia Carvalho

Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines. less

关键词： Liquid Chromatography (LC) Mass Spectrometry Stable Isotope Labeling Proteomics Protein Array Data analysis programming language Peptide quantitation Label-free quantitation Protein quantitation

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A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes

A Practical Guide for Comparative Genomics of Mobile Genetic...

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作者： Danillo Oliveira Alvarenga Leandro M. Moreira Mick Chandler Alessandro M. Varani

Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses. less

关键词： CRISPR Genomics Rearrangement Genome Annotation Statistical Calculation NCBI BLAST Genome Visualization GenBank programming language Python Pull-down Assay Evolution Transposons Genomic islands Insertion sequences Prophages Integrons Integrative conjugative elements

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Gas Chromatography–Mass Spectrometry (GC–MS) Analysis of

Gas Chromatography–Mass Spectrometry (GC–MS) Analysis of

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作者： Bahgat Fayed Ghalia Kohder Sameh S. Soliman

Unique metabolic features allow fungi to colonize and persist within the human host. Investigations of unique metabolic fingerprints of a pathogenic fungus can provide a more complete understanding of the infection process and an interpretation of associations between genotype and phenotype. Gas chromatography–mass spectrometry (GC–MS) has proved to be one of the most powerful analytical techniques used for qualitative and quantitative detection of cellular metabolites. This technique has been used for comparative metabolomic analyses of both intracellular and secreted metabolites under variable conditions. This book chapter describes the use of GC–MS in the detection of both intracellular and secreted metabolites from Candida auris, a newly emerging fungal pathogen representing a serious global health threat due to its multidrug resistance profile. The identified fungal metabolites are compared using available software in order to assign a correlation between the pattern of accumulation of metabolites and behavior of the organism. less

关键词： Spectroscopy Metabolomics Data analysis Statistical Calculation Sonication Machine Learning programming language Principal Component Analysis GraphPad Prism Chromatography Candida Candida albicans Saccharomyces cerevisiae GC–MS Metabolic profiling

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Chemical Informatics: Using Molecular Shape Descriptors in Structure-Based Drug Design

Chemical Informatics: Using Molecular Shape Descriptors in S...

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作者： Andy Jennings

The concept of molecular shape has been considered in various forms in the context of drug design. The following chapter details the application of molecular shape to the design of compound libraries for assessment of potential biological activity. Whilst the utility of shape descriptors is well documented in the area of ligand similarity, the use of shape descriptors is equally applicable to protein structures. Indeed, work has been published using various descriptors to compare proteins but little published where protein shape descriptors have been used to investigate ligand selectivity. less

关键词： Virtual Screening Rapid Overlay Of Chemical Structures Statistical Calculation Python programming language Data analysis Structure-based drug design Molecular Shape Combinatorial design Computational Chemistry Bioisostere.

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Sequence Handling by Sequence Analysis Toolbox v1.0

Sequence Handling by Sequence Analysis Toolbox v1.0

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作者： Christian Ravnsborg Ingrell Rune Matthiesen Ole Nørregaard Jensen

The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl inositol-anchored proteins. less

关键词： Sequence Analysis Mass Spectrometry High-Throughput Sequencing Structure Prediction Tandem Mass Spectrometry Swiss-Prot Expasy programming language Isoelectric point hydropathicity index transmembrane segments glycosylphosphatidyl inositol-anchored proteins

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EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

EzMechanism: an automated tool to propose catalytic mechanis...

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作者： Antonio J. Ribeiro Ioannis G. Riziotis Jonathan D. Tyzack Neera Borkakoti Janet M. Thornton

Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as ‘Easy’ Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic catalytic *** the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as ‘Easy’ Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic ca

关键词： Python programming language Cytoscape Computational models Software Protein function predictions Enzymes

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Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-Strand-Specific RNA-Seq Data

Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-S...

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作者： A. A. Golicz

Long noncoding RNAs (lncRNAs) are transcripts over 200 base pairs in length without discernible protein coding potential. Long intergenic noncoding RNAs (lincRNAs) constitute a subset of lncRNAs, which do not overlap protein coding genes. Here we describe a detailed pipeline for lincRNA discovery from publicly available non-stranded RNA-Seq datasets. The pipeline presented can be applied to any plant species for which RNA-Seq data and a reference genome sequence are available. less

关键词： RNA-seq Genome Annotation Statistical Calculation Genome-Wide Association Study StringTie HISAT Python programming language Oryza sativa Transcriptome lincRNA Long intergenic noncoding RNA

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Proton Nuclear Magnetic Resonance (

Proton Nuclear Magnetic Resonance (

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作者： Niraj Kumar Srivastava

Proton nuclear magnetic resonance spectroscopy (1H NMR) is a useful tool for the analysis of lipid components in biofluids such as serum/plasma. Such tool is applied for the analysis of lipid components in serum/plasma of patients with Duchenne muscular dystrophy (DMD). The practical approach of sampling, storage, lipid extraction procedure, sample preparation before performing the 1H NMR spectroscopy experiments is presented. All the experimental parameters of NMR spectroscopy are also described. Details of the assignments of lipid components (qualitative analysis) and quantification of particular lipid components (quantitative analysis) are explained. less

关键词： NMR Metabolomics Proton NMR Sonication 1D NMR Spectroscopy Two dimensional correlation spectroscopy 1H--1H Correlation Spectroscopy High-field NMR programming language Data analysis Cholesterol Phospholipids Muscular dystrophy Triglycerides DMD

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A Beginner’s Guide to the COBRA Toolbox

A Beginner’s Guide to the COBRA Toolbox

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作者： Ali Navid

COBRA toolbox is one of the most popular tools for systems biology analyses using genome-scale metabolic reconstructions. The toolbox permits the use of many constraint-based analytical methods for examining characteristics of metabolism in the biosystems ranging in complexity from single cells to microbial communities and ultimately multicellular organisms. The toolbox has a number of different variants that can be used depending on a user’s choice of programming language. Here, I provide a basic tutorial for beginners that plan to use the original MATLAB version of the toolbox. less

关键词： MATLAB Gene Knockout Metabolic Engineering programming language Escherichia coli Systems biology, Genome-scale models, Constraint-based analysis, FBA, Metabolic networks, COBRA toolbox

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Interfering Peptides Targeting Protein–Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence

Interfering Peptides Targeting Protein–Protein Interactions...

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作者： Alexander Hofmann Alexander Minges Georg Groth

Interfering peptides (iPs) have been recognized as valuable substances to specifically target protein–protein interactions (PPIs) in senescence and disease. Although the concept of iPs has been validated for several PPIs in medical and pharmaceutical research, little attention so far has been paid to the enormous potential iPs that may provide to target and control plant growth and developmental processes or plant environmental responses. However, recent research on PPIs in the ethylene signaling pathway has identified the synthetic peptide NOP-1 derived from the nuclear localization signal of ethylene regulator EIN2 as an efficient inhibitor of typical ethylene responses such as ripening, aging, and senescence. Biophysical and biochemical studies on purified recombinant proteins of the ethylene receptor family from various plant species demonstrate that the synthetic peptide binds in the nM-μM range at the plant target. Here, we describe methods to evaluate and quantify the effect of the NOP-1 peptide on flower senescence as a typical ethylene response in the intact plant system. This approach will help to systematically advance our technological capability to delay plant ethylene responses and to expand shelf-life or vase life of fruits and flowers. less

关键词： Spectroscopy HPLC Python Data analysis programming language Rubus idaeus Protein–protein interactions Interfering peptides Ethylene signaling Plant senescence

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