Extended Data Fig. 3: Classification output and MS method comparison.
From: SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry
a, Bar plots indicating the number of compartment classifications for the three different MS approaches used. b, Box plots displaying the classification probabilities for compartment-level classifications for the three different MS methods used. c, Box plots showing the minimum number of PSMs used for quantification of proteins on the basis of neighborhood classification agreement between HiRIEF and high-pH strategies (left) or HiRIEF and long-gradient strategies (right). Wilcoxon signed-rank test (two-sided) was used to calculate P values. d, Bar plots indicating the neighborhood classification agreement between methods for proteins quantified with one to two PSMs or more than two PSMs. e, Bar plots showing number of classifications and classification frequency of proteins binned by quantitative range (maximum value through minimum value in fractionation profile) for different MS approaches. Quantitative data are binned into five portions ranging between 0–0.5, 0.5–1, 1–1.5, 1.5–2 and >2. The elements of the boxplots in the figure are as follows: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers.
