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Updated: Jun 1, 2026
10:12
Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot
Published on: October 28, 2021
Preview: a program for surveying shotgun proteomics tandem mass spectrometry data
Yong J Kil1, Christopher Becker, Wendy Sandoval
1Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304, USA.
Analytical Chemistry
|May 31, 2011
Summary
Preview software improves peptide identification in tandem mass spectrometry by analyzing mass spectra for errors and modifications. This tool enhances parameter selection, leading to approximately 50% more confident identifications and phosphorylation site discoveries.
Area of Science:
- Proteomics
- Biochemistry
- Computational Biology
Background:
- Peptide identification via tandem mass spectrometry relies on user-defined parameters.
- Incorrect parameter choices can lead to missed identifications and erroneous results in proteomics research.
Purpose of the Study:
- To introduce Preview, a software tool designed to aid in selecting optimal parameters for peptide identification.
- To enhance the accuracy and completeness of peptide identifications in mass spectrometry data analysis.
Main Methods:
- Preview analyzes mass spectra for mass errors, digestion specificity, and known/unknown modifications.
- The software optionally recalibrates mass-to-charge measurements for improved data quality.
Main Results:
- Preview facilitates more informed parameter selection for database searches.
- Application of Preview in a Bruton's tyrosine kinase study increased confident identifications by ~50%.
- The number of identified phosphorylation sites also improved by approximately 50%.
Conclusions:
- Preview software significantly enhances the reliability and yield of peptide identification in tandem mass spectrometry.
- This tool assists researchers in optimizing data analysis, leading to more robust proteomic findings.
Related Concept Videos
01:21Tandem Mass Spectrometry
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01:33Peptide 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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Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...