Extended Data Fig. 4: Comparison of classification output for different MS approaches.
From: SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry
a, Density plots showing the minimum number of PSMs used for quantifications of proteins. Density plots are colored on the basis of agreement between HiRIEF and high-pH MS strategies: yellow if protein classification is the same in both methods, red if it is different, blue if the protein is unclassified in one of the methods and green if unclassified in both methods. b, Scatter plot showing the maximum neighborhood classification probability score of HiRIEF and high-pH methods and the minimum number of PSMs used for quantification between HiRIEF and high-pH methods. Proteins are colored on the basis of classification agreement as described above (a). c, SubCellBarCodes for APC protein from the original five cell lines analyzed and available in the SubCellBarCode.org resource. The left figure indicates neighborhood-level classifications, and the right figure indicates compartment-level classifications. d, Scatter plots showing classification probability of proteins for HiRIEF and long-gradient MS strategies (left) and high-pH and long-gradient MS strategies (right). Proteins are colored on the basis of classification agreement: yellow indicates the same classification in both methods, red indicates a different classification, blue indicates proteins that were unclassified in one of the methods and green indicates proteins that were unclassified in both methods. class., classified; grad., gradient; Unclass., unclassified.
