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A comprehensive full factorial LC-MS/MS proteomics benchmark data set.
SourceProteomics, 12, 14, (2012), pp. 2276-2281
1 augustus 2012
Article / Letter to editor
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Laboratory of Genetic, Endocrine and Metabolic Diseases
Paediatrics - OUD tm 2017
SubjectAnalytical Chemistry; IGMD 3: Genomic disorders and inherited multi-system disorders NCMLS 4: Energy and redox metabolism; IGMD 8: Mitochondrial medicine; IGMD 8: Mitochondrial medicine NCMLS 4: Energy and redox metabolism; IGMD 9: Renal disorder NCMLS 4: Energy and redox metabolism; IGMD 9: Renal disorder NCMLS 5: Membrane transport and intracellular motility; IGMD 8: Mitochondrial medicine NCMLS 4: Energy and redox metabolism; IGMD 9: Renal disorder NCMLS 5: Membrane transport and intracellular motility
An important prerequisite for the development and benchmarking of novel analysis methods is a well-designed comprehensive LC-MS/MS data set. Here, we present our data set consisting of 59 LC-MS/MS analyses of 50 protein samples extracted individually from Escherichia coli K12 and spiked with different concentrations of bovine carbonic anhydrase II and/or chicken ovalbumin, according to a 2 x 3 full factorial design. Using the well-annotated and commonly used E. coli proteome as the sample background ensures that the complexity of the data is on a par with most current proteomic analyses. Data were acquired over a 2-month period using multiple reversed-phase columns and instrument calibrations to include real-life challenges faced when analyzing large proteomics data sets. Moreover, so-called "ground truth" data, comprised by LC-MS/MS measurements of the pure spikes are included in the data set. The current manuscript elaborates this comprehensive benchmark data set for future development and evaluation of analysis methods and software.
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