1. S1. Typical appearance of a polyacrylamide gel slurry obtained by manual gel crushing with a pipette tip (Panel 1) and controlled shredding in a Gel Shredder (Panel 2). Please note uniform 150-300 µm gel fragments in Panel 2. 200 µm 200 µm

2. S2. Empirical cumulative distribution functions of calculated hydrophobicity of peptides exclusively identified in either standard in-gel digestion protocol or using the Gel Shredder. Peptide hydrophobicity was approximated using SSRCalc [25]. E.g. 80% of all peptides identified in the standard protocol have hydrophobicity equal or lower than 36 while for Gel Shredder it is 42. Standard protocol Shredder Hydrophobicity Percentage of peptides with hydrophobicity lower or equal to a given value 0 20 40 60 80 100

3. S2. Continued Non-parametric two sample Kolmogrov-Smirnov test was applied to test the hypothesis that distributions of hydrophobicity of peptides exclusively identified using either the standard protocol or the Gel Shredder are not equal. Specifically, it is assumed that peptides identified using the Gel Shredder are more hydrophobic, i.e. one-tailed test (p=0.015).