Fig. 7: Identification of mouse teratoma-derived proteins in serum.
From: Proteomics of protein trafficking by in vivo tissue-specific labeling
a, b Teratoma and serum log2(BirA*G3-ER/wt) TMT ratios in three replicates. Each point is n = 3 comparisons, mean ± SEM log2TMT ratio. The points are colored by the enrichment score (E-S): the number of comparisons (from 9) in which TMT-ratio > threshold (score 9 is for most confident hits [red] and 0 is background [black]). c, d As the E-S increases, the fraction of proteins with putative signal peptides increases. Two-sided Fisher’s exact test. Teratoma p-values (****) from left to right (c): 5.11 · 10−198, 7.86 · 10−221, 1.03 · 10−232, 5.11 · 10−241, 2.05 · 10−230, 1.66 · 10−216, 4.73 · 10−194, 3.10 · 10−167. Serum p-values (****) from left to right (d): 1.00 · 10−30, 3.61 · 10−33, 1.82 · 10−35, 2.48 · 10−35, 1.23 · 10−36, 1.37 · 10−31, 1.63 · 10−24, 8.42 · 10−18. e, f BirA*G3-ER;Cre teratoma and serum hits were enriched for lower-abundance proteins. Protein abundance information was from an integrated entire organism PAX database for mouse67. Frequency vs log10 protein abundance plots. For representation, serum and teratoma data are shown as histograms with equal bin sizes with B-spline smooth fits (calculated using OriginPro 2020). Statistics were performed on original data. Kruskal–Wallis test and Benjamini, Krieger, Yekutieli Linear Two-Stage Step-Up FDR (two-tailed p-value). Teratoma p-values (****) from top to bottom (e): 0.000071, 0.000025, 0.000009, 6.72 · 10−12, 4.26 · 10−11, 4.26 · 10−11, 1.02 · 10−8, 6.79 · 10−7. Serum p-values (****) from top to bottom (f): 0.0004, 0.0005, 0.0005, 0.0005, 0.0005, 0.0009, 0.0041, 0.0204. g–i As the E-S increases, the fraction of serum hits that were identified in the teratoma increases (g–h colored as red in g). Proteins with increased scores are not enriched for proteins found in previous whole blood (cells removed) proteomics (i) (see “Methods” section). Two-sided Fisher’s exact test. p-values from left to right (h): 0.0044, 0.0002, 0.000025, 0.000005, 0.000012, 0.000005, 0.000001, 0.0001. p-values from left to right (i; N.S. means non-significant): 0.9161, 0.9136, 0.8243, 0.9093, >0.9999, 0.7987, 0.0850, 0.2001. See also: Supplementary Figs. 14 and 15a–n, Supplementary Table 9, Supplementary Data 4–6. Source data are provided as a Source Data file.
