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Table 3 High-scoring proteins of interest identified by TMT 3D–LC–MS/MS profiling

From: Discovery of non-invasive biomarkers for the diagnosis of endometriosis

Acc. No. Description Biomarker score Protein score Unique peptides PSMs Ratio ES/CS Ratio ES/PS Ratio EP/CP Ratio EcS/ES Ratio PS/CS
P14384 Carboxypeptidase M CPM 26 154 2 6 1.619 2.525 2.451 0.319 0.633
P26599 Polypyrimidine tract-binding protein 1 PTBP1 24.6 264 7 11 2.646 2.771 0.953 0.377 0.787
Q14764 Major vault protein MVP 23 151 3 7 0.143 0.158 0.425 10.978 0.894
P29373 Cellular retinoic acid-binding protein 2 CRABP2 23 83 2 3 2.078 1.612 2.544 1.436 1.382
Q01995 Transgelin TAGLN 22.2 2119 17 95 1.105 1.324 2.171 18.832 1.240
Q01105 Protein SET 22.2 937 6 29 0.914 0.919 1.084 0.330 0.881
P00915 Carbonic anhydrase 1 CA1 22 5011 14 263 2.086 2.902 0.933 1.285 0.627
O94788 Retinal dehydrogenase 2 ALDH1A2 21.4 301 9 12 0.838 0.898 1.542 0.456 0.903
P16949 Stathmin STMN1 21.2 293 7 16 1.044 0.926 1.411 0.471 0.994
Q13308 Tyrosine-protein kinase 7 PTK7 21.2 362 3 13 0.510 0.677 1.497 0.293 0.807
P06703 Protein S100A6 21 762 5 47 1.379 1.653 0.795 3.364 0.774
P09466 Glycodelin PAEP 20.6 698 2 18 0.622 0.863 0.950 0.210 0.705
P02751 Fibronectin FN1 20.4 251 8 9 2.706 1.288 0.630 2.104 2.005
Q96KP4 Cytosolic non-specific dipeptidase CNDP2 20.2 1519 16 43 0.724 1.078 0.535 0.333 0.710
P00167 Cytochrome b5 CYB5A 20 692 7 29 0.835 0.880 0.205 0.979 0.948
P06401 Progesterone receptor PGR 20 37 1 1 1.415 1.762 2.420 0.321 0.792
P59665 Neutrophil defensin 1 DEFA1 19.6 137 3 11 0.325 2.476 1.315 4.989 0.133
P17661 Desmin DES 19.6 4279 24 216 0.904 0.930 1.381 3.056 1.063
Q05682 Caldesmon CALD1 19.4 677 6 25 1.162 0.950 1.260 7.685 1.223
Q7KZ85 Transcription elongation factor SPT6 SUPT6H 19.4 53 1 6 2.143 3.101 0.960 0.843 0.682
Q9HC84 Mucin-5B MUC5B 19.2 471 12 18 0.193 3.853 0.386 0.650 0.088
P12111 Collagen alpha-3(VI) chain COL6A3 19 687 12 27 1.933 1.254 1.209 18.478 1.597
P51884 Lumican LUM 19 1340 13 51 1.021 0.952 1.216 14.892 1.033
P60660 Myosin light polypeptide 6 MYL6 19 2726 12 92 1.378 0.878 1.148 5.003 1.382
P20774 Mimecan OGN 18.6 731 9 28 0.831 0.798 1.212 20.121 0.905
P09493 Tropomyosin alpha-1 chain TPM1 18.6 4361 8 186 1.004 1.007 1.245 10.119 0.964
P07951 Tropomyosin beta chain TPM2 18.6 4277 6 178 0.988 1.032 1.239 9.162 0.913
P06702 Protein S100A9 18.6 286 3 7 0.406 7.751 2.632 7.255 0.061
P67936 Tropomyosin alpha-4 chain TPM4 18.4 4288 12 201 1.014 1.023 1.230 7.301 0.918
P24821 Tenascin TNC 18.4 83 5 5 1.817 1.682 1.502 1.151 1.022
O00264 PGRMC1 18.4 191 4 8 1.013 1.035 1.561 0.609 1.228
P52907 F-actin-capping protein subunit a1 CAPZA1 18.2 145 4 7 3.031 1.078 0.885 1.459 1.280
P51888 Prolargin PRELP 18 84 3 5 0.504 0.471 1.466 33.466 1.145
Q05707 Collagen alpha-1(XIV) chain COL14A1 18 1210 18 49 1.294 0.834 0.898 10.120 1.426
P21333 Filamin-A FLNA 18 2103 41 77 1.227 0.967 1.509 2.216 1.357
P22105 Tenascin-X TNXB 18 85 3 3 1.548 1.570 1.155 2.143 0.973
P04792 Heat shock protein beta-1 HSPB1 17.8 1495 8 69 1.298 0.775 1.077 4.369 1.586
Q12805 Protein EFEMP1 17.6 62 2 3 2.222 1.596 0.921 1.974 1.373
Q32P28 Prolyl 3-hydroxylase 1 LEPRE1 17.6 139 3 4 1.399 1.023 1.415 0.547 1.260
P21291 Cysteine and glycine-rich protein 1 CSRP1 17.4 489 6 17 0.912 1.039 1.080 21.887 0.735
P02452 Collagen alpha-1(I) chain COL1A1 17.4 830 11 45 1.124 0.428 0.904 5.938 2.536
P18206 Vinculin VCL 17.4 1911 29 73 1.404 0.904 1.131 2.429 1.425
P35749 Myosin-11 MYH11 17.2 1059 14 40 0.986 1.006 1.228 3.765 1.372
P12004 Proliferating cell nuclear antigen PCNA 17.2 107 4 7 0.954 0.709 1.790 0.414 1.326
  1. Selection of proteins with biomarker score, protein score, numbers of unique peptides and peptide spectrum matches (PSMs) and ratios of expression for the different tissue comparisons. Proteins in italics are of particular note with several selected for serum testing