Number of peptides identified following different extraction procedures and different MS methods. In each rectangle, the figure lists for a particular extraction procedure a range of the number of detected peptides. Because the number of detected peptides differed for the 2 types of MS techniques applied, we list a range. The investigated proteins are grouped, as abbreviated in the right column: GPI, GPI-anchored proteins; LMA, loosely membrane-associated proteins; TMA, tightly membrane-associated proteins; IMP, integral membrane protein; CYTO, cytoskeletal proteins; and GLYCO, glycolytic proteins. Proteins are shown in green or dark yellow to maintain the consistent statistical color-coding adopted in the supplementary tables, where green proteins are detected in almost all runs and tan in a high number of runs. To illustrate the most dramatic differences among “membrane proteins” following extractions, an area is highlighted in blue.