Data underlying the figures in the publication “In-Droplet Electrophoretic Separation and Enrichment of Biomolecules”, published in Anal. Chem. 2020, 92, 12, 8414–8421. https://pubs.acs.org/doi/10.1021/acs.analchem.0c01044 Table of contents: 1. Figure 2 – Analyte Enrichement; Zip. archive containing (1) experimental videos of in-droplet separation for nine analytes at different electric fields, (2) the extracted fluorescence intensity values of the videos, and (3) the average enrichment factor. 2. Figure 3 – Electrode Length; Zip. archive containing (1) experimental videos of in-droplet separation when (a) HPMC, (b) buffers with different ionic strengths, and (c) different analyte concentrations are used, (2) the extracted fluorescence intensity values of the videos, and (3) the average enrichment factor. 3. Figure 4 – Extra Parameters; Zip. archive containing (1) experimental videos of in-droplet separation when (a) HPMC, (b) buffers with different ionic strengths, and (c) different analyte concentrations are used, (2) the extracted fluorescence intensity values of the videos, and (3) the average enrichment factor. 4. Figure 5 – Size and Velocity; Zip. archive containing (1) experimental videos of in-droplet separation for dichlorofluorescein at different droplet geometries and velocities, (2) the extracted fluorescence intensity values of the videos, and (3) the average enrichment factor. 5. Figure 6 – Mass Spectrometry; Zip. archive containing the mass spectrum of anodic and cathodic droplets after the in-droplet separation and splitting.