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Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

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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Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue

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Two-dimensional target decoy strategy for shotgun proteomics.

Marshall W Bern¹, Yong J Kil

¹Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304, United States. bern@parc.com

Journal of Proteome Research

|October 21, 2011

Summary

This summary is machine-generated.

This study introduces a new target-decoy strategy for shotgun proteomics that simultaneously controls false discovery rates (FDR) at both peptide-to-spectrum match (PSM) and protein levels, improving data reliability.

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Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

The target-decoy approach is standard for estimating and controlling false discovery rate (FDR) in shotgun proteomics.
Current methods control FDR at either the peptide-to-spectrum match (PSM) or protein level, but not both simultaneously.
This necessitates different strategies based on the relative numbers of spectra and proteins, complicating data analysis.

Purpose of the Study:

To propose a novel variation of the target-decoy strategy.
To enable simultaneous estimation and control of PSM and protein FDRs.
To offer a unified approach irrespective of the ratio of spectra to proteins.

Main Methods:

A modified target-decoy strategy is presented.
The method estimates and controls both PSM-level and protein-level FDRs concurrently.
The approach is validated across different data scenarios.

Main Results:

The proposed two-dimensional strategy effectively controls both PSM and protein FDRs simultaneously.
This unified approach is advantageous regardless of the number of spectra versus proteins.
The method offers benefits even when the primary goal is a PSM list with controlled FDR.

Conclusions:

A single, versatile target-decoy strategy can manage FDR at both PSM and protein levels.
This simplifies data analysis in shotgun proteomics.
The proposed method enhances the reliability of proteomic data identification.