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Peptide Identification Using Tandem Mass Spectrometry01:33

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Eric W Deutsch1, Zhi Sun1, David S Campbell1

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

Journal of Proteome Research
|September 1, 2016
PubMed
Summary
This summary is machine-generated.

Selecting the right protein sequence database is crucial for shotgun proteomics. This study introduces tiered human databases, improving peptide identification with a slight increase in computational cost for variant discovery.

Keywords:
humansearch databasesshotgun mass spectrometry

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Genomics

Background:

  • Shotgun proteomics mass spectrometry data analysis is sensitive to the chosen protein sequence database.
  • Multiple, sometimes conflicting, sequence databases exist for many species, particularly for human samples.
  • Current databases are genome-based, compiling predicted gene and protein sequences.

Purpose of the Study:

  • To create and provide a unified set of primary human protein sequence databases from diverse sources.
  • To develop tiered databases of increasing completeness for mass spectrometry-based proteomics.
  • To evaluate the utility of these tiered databases for peptide identification.

Main Methods:

  • Compiled four tiered human protein sequence databases of varying sizes, from minimal to comprehensive.
  • Analyzed proteomics data from HeLa cells and human liver tissue using each of the four database tiers.
  • Assessed the impact of database complexity on peptide identification rates and computational cost.

Main Results:

  • Tiered Human Integrated Search Proteome (THISP) databases were created, ranging from Tier 1 (primary isoforms) to Tier 4 (comprehensive non-redundant sequences).
  • Using Tiers 2, 3, and 4 identified approximately 0.8%, 1.1%, and 1.5% more peptides, respectively, compared to Tier 1.
  • Increased peptide identification came with higher computational costs, particularly beneficial for identifying sequence variants.

Conclusions:

  • Tiered databases offer a trade-off between identification depth and computational expense in proteomics.
  • A strategy of searching simpler databases first, then verifying with complex ones, is effective.
  • An automated system provides monthly updated search databases at http://www.peptideatlas.org/thisp/ for community use.