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Related Concept Videos

Proteomics01:33

Proteomics

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 proteomics...
Statistical Package for the Social Sciences (SPSS)01:22

Statistical Package for the Social Sciences (SPSS)

The Statistical Package for the Social Sciences, or SPSS, is a data management and analysis software suite. Developed by SPSS Inc. in 1968 and acquired by IBM in 2009, this tool was initially designed for social science data analysis, evolving to serve a wider range of disciplines. It was later renamed to Statistical Product and Service Solutions.
SPSS streamlines the process from data preparation to analysis and reporting. It is characterized by its user-friendly interface, which conceals...
The Unfolded Protein Response01:37

The Unfolded Protein Response

The ER is the hub of protein synthesis in a cell. It has robust systems to quality control protein folding and also for degradation of terminally misfolded proteins. Under normal conditions, a small proportion of misfolded proteins that cannot be salvaged need to be transported to the cytoplasm by the ER-associated degradation or ERAD pathways. However, if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding...
Electrospray Ionization (ESI) Mass Spectrometry01:12

Electrospray Ionization (ESI) Mass Spectrometry

Higher molecular weight biomolecules are nonvolatile compounds that may decompose before ionizing or vaporizing during mass analysis with conventional electron impact ionization methods. Accordingly, electrospray ionization (ESI) is the favored method for vaporizing and ionizing biomolecules as it circumvents rapid fragmentation and enables the recording of mass signals for the entire biomolecule.
ESI utilizes electrical energy to transfer ions from the liquid phase of the sample into the...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
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Published on: May 16, 2017

SPIRE: Systematic protein investigative research environment.

Eugene Kolker1, Roger Higdon, Phil Morgan

  • 1Bioinformatics & High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, WA, USA. Eugene.Kolker@seattlechildrens.org

Journal of Proteomics
|May 26, 2011
PubMed
Summary

The Systematic Protein Investigative Research Environment (SPIRE) enhances proteomics analysis by integrating multiple search engines and providing accurate error estimation. This user-friendly platform improves protein identification and functional annotation for biological research.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Mass spectrometry (MS) based proteomics is crucial for biological research.
  • Existing proteomics analysis tools often lack integration and user-friendliness.
  • Accurate false discovery rate estimation is essential for reliable protein identification.

Purpose of the Study:

  • To introduce the Systematic Protein Investigative Research Environment (SPIRE) as a web-based platform for experiment-specific proteomics analysis.
  • To highlight SPIRE's focus on usability, integration of analytical tools, and experimental design-based analysis.
  • To demonstrate SPIRE's capability in improving protein identification and functional annotation.

Main Methods:

  • SPIRE integrates multiple open-source search engines (X!Tandem, OMSSA, SpectraST) and data analysis methods.
  • Novel methods are employed for generating false discovery rates (FDR) and local false discovery rates (LFDR).
  • The platform analyzes data based on experimental design, not just runs, and connects results to functional and expression data.

Main Results:

  • Integration of X!Tandem, OMSSA, and SpectraST in SPIRE increased protein identifications by 52-88% compared to single engines.
  • SPIRE provides accurate multi-faceted error estimation.
  • Demonstrated SPIRE's utility by analyzing mitochondrial proteins from wild type and mutant C. elegans.

Conclusions:

  • SPIRE offers a user-friendly, integrated approach to proteomics analysis, enhancing protein identification and error estimation.
  • The platform facilitates the interpretation of proteomics data by linking it to protein function, pathways, and expression from model organisms.
  • SPIRE supports analysis and annotation of user-supplied protein ID and expression data, broadening its applicability.