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. 2024 Oct 11;96(42):16861–16870. doi: 10.1021/acs.analchem.4c03625

Figure 2.

Figure 2

Summary and differential abundance analysis of LC-MS/MS data from microextractions. A. The number of unique proteins identified in colon, ovary, and pancreas samples without thermal denaturation (blue) and with thermal denaturation (purple). B. The number of unique peptides identified in colon, ovary, and pancreas samples without thermal denaturation (blue) and with thermal denaturation (purple). C. The Global Average of Hydropathy (GRAVY) value for identified peptides from nondenatured (blue) and thermally denatured (purple) samples in the colon, ovary, and pancreas in which a higher GRAVY score indicates higher average hydrophobicity. Student’s T-Test result **** P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. Differential abundance analysis of LC-MS/MS data using label-free quantitation comparing nondenatured and thermally denatured (TD) colon (D,E,F) and ovary (G,H,I). Pancreas tissue was omitted from this analysis because nondenatured pancreas tissue had insufficient protein identifications for statistical comparison. D. Volcano plot visualizing proteins more abundant (in purple) and less abundant (in blue) in TD colon. Proteins with increased abundance in TD tissue included Collagens alpha-1(I), alpha-2(I), alpha-1(III), alpha-1(IV), and alpha-2(IV) (CO1A1, CO1A2, CO3A1, CO4A1, CO4A2), Plectin, Myosin-9 (MYH9), Filamin-A (FLNA), Supervillin (SVIL), and Fibrillin-1 (FBN1). Proteins with decreased abundance in the TD colon include SH3 domain-binding glutamic acid-rich-like protein (SH3L1), Rho GDP-dissociation inhibitor 1 (GDIR1), Heat shock protein beta-1 (HSPB1), 60S ribosomal protein L7a (RL7A), Apolipoprotein A-I (APOA1), 10 kDa heat shock protein (CH10, HSPE1), Annexin A2 (ANXA2), Myosin regulatory light polypeptide 9 (MYL9), Ras-related protein R-Ras (RRAS). E. Gene ontology (GO) analysis representing the protein class of proteins less abundant in TD colon. F. GO analysis of proteins more abundant in TD colon. G. Volcano plot visualizing proteins more abundant (in purple) and less abundant (in blue) in TD ovary. Proteins more abundant in TD ovary include Endoplasmic reticulum chaperone BiP (BiP), Plectin, Probable ATP-dependent RNA helicase (DDX17), collagens alpha-1(VI), alpha-2(VI), alpha-3(VI), alpha-1(XII), alpha-2(I), (CO6A1, CO6A2, CO6A3, COCA1, CO1A2), Tubulin beta-4B chain (TBB4B), Filamin-A (FLNA), Heat shock cognate 71 kDa protein (HSP7C), Immunoglobulin heavy constant gamma 1 (IGHG1), and Actin (ACTG). Proteins less abundant in TD ovary include RNA-binding protein FUS (FUS), Heterogeneous nuclear ribonucleoprotein K (HNRPK), 40S ribosomal protein S8 (RS8), Neuroblast differentiation-associated protein (AHNK), Y-box-binding protein 1 (YBOX1), RNA-binding motif protein (RBMX), Histone H2A type 1-J (H2A1J), Heterogeneous nuclear ribonucleoproteins C1/C2 (HNRPC). H. GO classes of proteins less abundant in TD ovary. I. Classes of proteins more abundant in TD ovary.