Fig. 2: Challenges and solutions for phosphoDIA. | Nature Communications

Fig. 2: Challenges and solutions for phosphoDIA.

From: Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

Fig. 2

a Confirming and refuting fragments for site localization. b Calculation of site localization confidence score. The score for a given site localization candidate is calculated by summing all confirming fragments matched and subtracting the sum of all refuting fragments matched. c Workflow to evaluate localization algorithm with MaxQuant. d Error rates for phosphorylation site assignment in DDA and DIA. e Coverage of assigned phosphorylation site in a diluted yeast background for DDA and DIA. Source data for this figure are provided as a Source Data file.

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