A method for improving SELDI-TOF mass spectrometry data quality

Details

• Alternative Title:
  Proteome Sci
• Personal Author:
  Whistler, Toni ; Rollin, Dominique ; Vernon, Suzanne D
• Description:
  Background
  
  Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) is a powerful tool for rapidly generating high-throughput protein profiles from a large number of samples. However, the events that occur between the first and last sample run are likely to introduce technical variation in the results.
  
  Methods
  
  We fractionated and analyzed quality control and investigational serum samples on 3 Protein Chips and used statistical methods to identify poor-quality spectra and to identify and reduce technical variation.
  
  Results
  
  Using diagnostic plots, we were able to visually depict all spectra and to identify and remove those that were of poor quality. We detected a technical variation associated with when the samples were run (referred to as batch effect) and corrected for this variation using analysis of variance. These corrections increased the number of peaks that were reproducibly detected.
  
  Conclusion
  
  By removing poor-quality, outlier spectra, we were able to increase peak detection, and by reducing the variance introduced when samples are processed and analyzed in batches, we were able to increase the reproducibility of peak detection.
  
  
• Subjects:
  Methodology
• Source:
  Proteome Sci. 2007; 5:14.
• Document Type:
  Journal Article
• Volume:
  5
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:300b48c24b6de20610e6b6328ddb07117ea60d351050c5c42e1935a676125c1d
• Download URL:
  https://stacks.cdc.gov/view/cdc/3558/cdc_3558_DS1.pdf
• File Type:
  [PDF - 557.21 KB ]