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Generic workflow for quality assessment of quantitative label‐free LC‐MS analysis
Author(s) -
Sandin Marianne,
Krogh Morten,
Hansson Karin,
Levander Fredrik
Publication year - 2011
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201000493
Subject(s) - workflow , computer science , software , reliability (semiconductor) , metric (unit) , data mining , quality (philosophy) , reliability engineering , database , engineering , power (physics) , operations management , physics , philosophy , epistemology , quantum mechanics , programming language
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.