Proteomics
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Rescooped by Robbie Tan from proteomics
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An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays

An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays | Proteomics | Scoop.it
The pace of genome sequencing is accelerating, revealing the genetic background of a growing number of organisms. However, assigning function to each nucleotide in a completed genome remains the rate-limiting step. New technologies in transcriptomics and proteomics have influenced the emergence of proteogenomics, a field at the confluence of genomics, transcriptomics, and proteomics. First generation proteogenomic toolkits employ peptide mass spectrometry to identify novel protein coding. These efforts rely heavily on existing algorithms designed for standard proteome analysis and fail to address the challenges specific to genome annotation. In this work we extend first generation proteogenomic tools to achieve greater accuracy and enable the analysis of large, complex genomes. We apply our pipeline to Zea mays, which has a genome comparable in size to human. Our pipeline begins with the comparison of mass spectra to a putative translation of the genome. Our translation includes the six-frame translation as well as a splice graph for capturing protein splice variants. We distribute the identification of mass spectra across 45 compute nodes for increased efficiency and employ a database-independent scoring method to improve sensitivity. We select novel peptides, those that match to a region of the genome that was not previously known to be protein coding, for grouping into events. Each of our eight event types describes a refinement needed to the genome annotation. We present a novel, Bayesian framework for evaluating the accuracy of each event. Our calculated event probability, or eventProb, considers the number of supporting peptides and spectra, and the quality of each supporting peptide-spectrum match. More than 80% of the maize genome is comprised of repetitive elements. To address this, our eventProb handles uniquely located peptides and shared location peptides separately. Our pipeline predicts 165 novel protein-coding genes and proposes updated models for 741 additional genes.
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Using Proteomics Analysis to Uncover Protein Glycosylation | Mirko ...

Using Proteomics Analysis to Uncover Protein Glycosylation | Mirko ... | Proteomics | Scoop.it
Our recent work on protein glycosylation has received attention from http://acceleratingscience.com. Following the full text. Protein recovered from poultry and fish by-products is becoming more important as an ingredient in ...
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- A powerful software library for proteomics now at researchers ...

- A powerful software library for proteomics now at researchers ... | Proteomics | Scoop.it
Reasearchers from the ISMB in collaboration with mineway GmbH have created Python-bindings for OpenMS, a powerful software library for mass spectrometry based proteomics. These Python tools allow researchers to run ...
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Danny Hillis: Understanding cancer through proteomics | Talk Video ...

Danny Hillis: Understanding cancer through proteomics | Talk Video ... | Proteomics | Scoop.it
Danny Hills makes a case for the next frontier of cancer research: proteomics, the study of proteins in the body. As Hillis explains it, genomics shows us a list of the ingredients of the body -- while proteomics shows us what those ingredients ...
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Proteomics identifies possible RCC biomarkers - News-Medical.net

Proteomics identifies possible RCC biomarkers - News-Medical.net | Proteomics | Scoop.it
Proteomics identifies possible RCC biomarkers News-Medical.net Quantitative label-free proteomics identified 596 proteins with significantly higher (eg, integrin-beta) or lower (eg, metallthionein) expression in the RCC samples than in the healthy...
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Comparative proteomic analysis of the Arabidopsis cbl1 mutant in response to salt stress (Proteomics)

Comparative proteomic analysis of the Arabidopsis cbl1 mutant in response to salt stress (Proteomics) | Proteomics | Scoop.it
Many environmental stimuli, including light, biotic and abiotic stress factors, induce changes in cellular Ca2+ concentrations in plants. Such Ca2+ signatures are perceived by sensor molecules such as calcineurin B-like (CBL) proteins. AtCBL1, a member of the CBL family which is highly inducible by multiple stress signals, is known to function in the salt stress signal transduction pathway and to positively regulate the plant tolerance to salt. To shed light into the molecular mechanisms of the salt stress response mediated by AtCBL1, a two dimensional DIGE proteomic approach was applied to identify the differentially expressed proteins in Arabibdopsis wild-type and cbl1 null mutant plants in response to salt stress. Seventy-three spots were found altered in expression by least 1.2-fold and 50 proteins were identified by MALDI-TOF/TOF MS, including some well-known and novel salt-responsive proteins. These proteins function in various processes, such as signal transduction, ROS scavenging, energy production, carbon fixation, metabolism, mRNA processing, protein processing and structural stability. Receptor for activated C kinase 1C (RACK1C, spot 715), a WD40 repeat protein, was up-regulated in the cbl1 null mutant, and two rack1c mutant lines showed decreased tolerance to salt stress, suggesting that RACK1C plays a role in salt stress resistance. In conclusion, our work demonstrated the advantages of the proteomic approach in studies of plant biology and identified candidate proteins in CBL1-mediated salt stress signaling network.
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Can genomics and proteomics help select better treatment for breast ...

Can therapy for advanced breast cancer be individualized based on proteomics and genomics data?
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ConQEST 2014: From research to reality: bringing proteomics to a ...

Session abstract: Proteomics is a rapidly expanding research area incorporating both biology and chemistry by focusing on the study of proteins. Although many of the 'cutting edge' research methods are beyond the capability ...
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Bottom-up and Shotgun Proteomics to Identify a... | Video Protocol

Bottom-up and Shotgun Proteomics to Identify a... | Video Protocol | Proteomics | Scoop.it
Proteomics is a commonly used approach that can provide insights into complex biological systems. The cochlear sensory epithelium contains receptors that transduce the mechanical energy of sound into an electro-chemical ...
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Less label, more free: Approaches in label-free quantitative mass spectrometry - Neilson - 2011 - PROTEOMICS - Wiley Online Library

Less label, more free: Approaches in label-free quantitative mass spectrometry - Neilson - 2011 - PROTEOMICS - Wiley Online Library | Proteomics | Scoop.it

In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled quantitation.


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