Parallel post-source decay for increasing protein identification confidence levels from 2-D gels

Asa Wahlander, Giorgio Arrigoni, Marten Snel, Ulf Hellman, Peter James

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

Peptide mass fingerprinting (PMF) has over the years become one of the most commonly used tools for high-throughput analysis and identification of proteins. This method is applicable when relatively simple samples have to be analysed and it is commonly used for analysing proteins previously separated by 2-DE. The most common type of instrument used for this approach is the MALDI-TOF that has proved to be particularly suitable for the PMF analysis because of its characteristics of speed, robustness, sensitivity and automation. We have used a MALDI-TOF equipped with a novel parallel PSD capability (MALDI micro MX), to perform the analysis of two sets of different biological samples isolated by 2-DE. By using a method that integrates the data obtained by PMF analysis with the PSD data obtained in the same experiment, we show that the new multiplexed PSD solution increases the protein identification rate compared to the normal PMF approach. We also investigated the use of a charge-directed fragmentation modification reagent to improve the identification rate and confidence levels.

Original languageEnglish
Pages (from-to)1771-1779
Number of pages9
JournalProteomics
Volume8
Issue number9
DOIs
Publication statusPublished - 1 May 2008
Externally publishedYes

Keywords

  • Confidence level
  • Database searching
  • Peptide mass fingerprinting
  • Post-source decay

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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