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Related Concept Videos

Proteomics01:33

Proteomics

9.9K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Disubstituted Cyclohexanes: cis-trans Isomerism02:37

Disubstituted Cyclohexanes: cis-trans Isomerism

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Depending upon the different spatial orientation of the substituents, the disubstituted cycloalkanes exhibit two types of stereoisomers. The cis isomers have the substituents on the same side of the ring, whereas the trans isomers have the substituents on the opposite sides. These stereoisomers exhibit different physical properties and cannot be interconverted without breaking the carbon-carbon bonds.
In cyclohexane, the substituents can occupy different positions generating distinct isomers....
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Labeling Emotion01:20

Labeling Emotion

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Emotional labeling is a cognitive process that involves identifying and naming one's emotions, such as anger, fear, happiness, or sadness. It allows individuals to recognize and express their internal emotional states, a critical aspect of emotional regulation and communication. Labeling emotions requires more than mere recognition; it also involves drawing upon memory and contextual cues to understand the current situation and apply a corresponding emotional label. For instance, feeling...
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Reduction of Alkynes to trans-Alkenes: Sodium in Liquid Ammonia02:10

Reduction of Alkynes to trans-Alkenes: Sodium in Liquid Ammonia

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Alkynes can be reduced to trans-alkenes using sodium or lithium in liquid ammonia. The reaction, known as dissolving metal reduction, proceeds with an anti addition of hydrogen across the carbon–carbon triple bond to form the trans product. Since ammonia exists as a gas (bp = −33°C) at room temperature, the reaction is carried out at low temperatures using a mixture of dry ice (sublimes at −78°C) and acetone. 
When dissolved in liquid ammonia, an alkali metal, such as sodium,...
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Labeling DNA Probes03:31

Labeling DNA Probes

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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
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Agonism and Antagonism: Quantification01:14

Agonism and Antagonism: Quantification

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When drugs are administered, they can elicit either an agonist or antagonist effect on the body. Agonism occurs when a drug activates a specific receptor, triggering a biological response. On the other hand, antagonism happens when a drug binds to the same receptors but blocks their activation, thereby preventing a biological response.
To quantify these effects, researchers use a dose-response curve, which provides valuable information about the potency and efficacy of a drug. Potency refers to...
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Related Experiment Video

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"Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome
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"Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome

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StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline.

Michael R Hoopmann1, Jason M Winget1, Luis Mendoza1

  • 1Institute for Systems Biology , Seattle, Washington 98109, United States.

Journal of Proteome Research
|February 6, 2018
PubMed
Summary

StPeter offers a new, integrated tool for label-free quantification in proteomics. This implementation within the Trans-Proteomic Pipeline provides reproducible, efficient, and high-quality relative abundance measures for shotgun proteomics data.

Keywords:
automationdata analysis pipelinelabel-free quantificationopen-source softwarequantitative proteomicstrans-proteomic pipeline

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Label-free quantification (LFQ) is increasingly vital for determining relative protein abundance in proteomics.
  • A lack of accessible and integrated tools has hindered widespread adoption of LFQ.
  • Existing methods often lack ease of use and reproducibility.

Purpose of the Study:

  • To introduce StPeter, an implementation of Normalized Spectral Index quantification.
  • To integrate StPeter into the widely used Trans-Proteomic Pipeline (TPP).
  • To provide an accessible, reproducible, and user-friendly LFQ tool for proteomics researchers.

Main Methods:

  • StPeter implements the Normalized Spectral Index (NSI) quantification method.
  • Integration into the Trans-Proteomic Pipeline (TPP) ensures broad availability.
  • The software was evaluated using a benchmark dataset for shotgun proteomics.

Main Results:

  • StPeter demonstrated superior performance compared to other state-of-the-art LFQ packages.
  • The tool is computationally efficient and supports diverse instrument platforms and experimental designs.
  • Results are viewable in TPP GUIs and exportable for downstream analysis.

Conclusions:

  • StPeter provides high-quality, reproducible label-free quantification.
  • Integration into the TPP simplifies and accelerates LFQ analysis.
  • This tool enhances accessibility for proteomics researchers performing relative abundance measurements.