Generic workflow for quality assessment of quantitative label-free LC-MS analysis

Research output: Contribution to journalArticle

Abstract

As high resolution instruments are becoming standard in proteomics laboratories, label-free quantification using precursor measurements is becoming a viable option, and is consequently rapidly gaining popularity. Several software solutions have been presented for label-free analysis, but to our knowledge no conclusive studies regarding the sensitivity and reliability of each step of the analysis procedure has been described. Here we use real complex samples to assess the reliability of label-free quantification using four different software solutions. A generic approach to quality test quantitative label-free LC-MS is introduced. Measures for evaluation are defined for feature detection, alignment and quantification. All steps of the analysis could be considered adequately performed by the utilized software solutions, although differences and possibilities for improvement could be identified. The described method provides an effective testing procedure, which can help the user to quickly pinpoint where in the workflow changes are needed.

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Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Immunology in the medical area

Keywords

  • quality control, LC-MS, label-free quantification
Original languageEnglish
Pages (from-to)1114-1124
JournalProteomics
Volume11
Issue number6
Publication statusPublished - 2011
Publication categoryResearch
Peer-reviewedYes