Figure 1.

Cell Surface Mass Spectrometry Yields Protein Abundance Profiles

(A) Cell production strategy involving embryoid body differentiation with cytokine addition at day 2 (d2) and d3 of differentiation. Cell types were assessed using flow cytometry with stage-specific markers (I–V). The number in the box represents the percent positive value.

(B) Surface proteins were labeled and processed into peptides using a cell surface capture procedure before LC-MS/MS analysis.

(C) Unsupervised k-means clustering of cell surface MS data was separated into 5 main clusters (red, upregulated; white, neutral; blue, downregulated; n = 4–5 in each group, pooled from 6 independent experiments). Line graph representations of each cluster show distinct profiles of up- and downregulation.