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Table 1 Comparison of targeted and non-targeted proteomics

From: Non-targeted proteomics of acute respiratory distress syndrome: clinical and research applications

  Advantages Disadvantages
Non-targeted proteomics a. Broad spectrum screening of disease-related proteins
b. Testing the samples and transitioning to targeted proteomics
c. To detect as many distinct features as possible in a single analysis and, combined with multivariate statistics, identify biomarkers which distinguish case from control groups
d. Allows larger scale studies of carefully phenotyped patients will identify novel pathophysiology in the disease
a. The target protein cannot be well screened for absolute quantitative and qualitative research and analysis
b. Not entirely unbiased. The lack of absolute quantification hampers benchmarking of ‘normal’ protein levels and ultimately interlaboratory comparison of results
c. False identification of proteins or bias/signal drift introduced from matrix effects may also occur due to a lack of standards
Targeted proteomics a. To study different subtypes of the same disease type and draw a clinical reference map of biological targeted proteins, so as to guide clinical treatment
b. Excellent analytical precision
c. Unequivocal identification that can serve individually and together as biomarkers of both subphenotypes of disease and disease prognosis
d. To reduce false positives which may lead to misinterpretation of an affected biological pathway
a. Limited coverage of the proteome which increases the risk of overlooking the proteomic response of interest.
b. When a narrower mass range was applied, these proteins were not observable in samples.
c. Limited resources and/or sample size and in the absence of prior knowledge on the protein of interest