Table 4.
Enrichment behavior of peptides and epitopes of autoimmune-related antigens.
| MaxQuant-peptides | Uniprot accession | PLAtEAU-epitopes | ||||||
|---|---|---|---|---|---|---|---|---|
| Sig. | −log(P) | Diff. | Sequence | Sig. | −log(P) | Diff. | Sequence | |
| 0.587 | −2.197 | DPPLIALDKDAPLRFA |
O94985 Calsyntenin |
+ | 2.502 | −3.742 | DPPLIALDKDAPLRFA | |
| 1.124 | −3.665 | ENDNTVLLDPPLIALDKDAP | ||||||
| 1.208 | −4.413 | ENDNTVLLDPPLIALDKDAPL | ||||||
| 0.467 | −0.721 | NDNTVLLDPPLIALDKD | ||||||
| 1.994 | −4.383 | NDNTVLLDPPLIALDKDAP | ||||||
| 1.925 | −4.465 | NDNTVLLDPPLIALDKDAPL | ||||||
| 0.112 | −0.461 | GKITSIVKDSSAARN |
O00560 Syntenin-1 |
0.389 | 0.086 | ITSIVKDSSAARN | ||
| 0.460 | −0.509 | GKITSIVKDSSAARNG | ||||||
| 1.419 | −1.538 | GKITSIVKDSSAARNGL | ||||||
| 0.053 | 0.065 | GKITSIVKDSSAARNGLL | ||||||
| 0.137 | −0.620 | ITSIVKDSSAARN | ||||||
| 1.535 | −5.911 | ITSIVKDSSAARNG | ||||||
| 1.350 | −1.670 | ITSIVKDSSAARNGL | ||||||
| 0.538 | −0.419 | ITSIVKDSSAARNGLL | ||||||
| 0.138 | −0.539 | KITSIVKDSSAARN | ||||||
| 0.099 | −0.137 | KITSIVKDSSAARNG | ||||||
| 0.763 | −1.545 | KITSIVKDSSAARNGL | ||||||
| 0.039 | 0.050 | KITSIVKDSSAARNGLL | ||||||
| 0.029 | −0.044 | NGKITSIVKDSSAARNG | ||||||
| 0.042 | 0.051 | NGKITSIVKDSSAARNGLL | ||||||
| 0.268 | −1.424 | SIVKDSSAARNGL | ||||||
| 1.746 | −4.972 | LEDLKVDKVIQAQTA | + | 3.230 | −5.318 | LEDLKVDKVIQAQTA | ||
| + | 4.777 | 7.012 | APPEVVMDPALAAQYEH |
P62826 GTP-binding nucl. Protein Ran |
+ | 8.732 | 7.461 | APPEVVMDPALAAQYEH |
| 0.460 | 1.769 | APPEVVMDPALAAQYE | ||||||
| 1.716 | 3.894 | APPEVVMDPALAAQYEHD | ||||||
| 0.165 | −0.158 | AAQGEPQVQFK | n.d. | |||||
| 0.116 | −0.387 | KKNLQYYDISAK | n.d. | |||||
| 0.020 | −0.084 | AEREIVRDIKEKL |
P60709 Actin B |
+ | 1.776 | 2.580 | AEREIVRDIKEKL | |
| 1.255 | 4.053 | AEREIVRDIKEKLCYV | ||||||
| 0.968 | −0.924 | DDDIAALVVDNGSGMCK | 0.000 | 0.000 | DDDIAALVVDNGSGMCKA | |||
| 1.940 | −4.570 | DDDIAALVVDNGSGMCKA | ||||||
| 0.256 | −0.882 | DDDIAALVVDNGSGMCKAG | ||||||
| 0.049 | 0.288 | DDDIAALVVDNGSGMCKAGFAGDDAPR | ||||||
| 1.105 | −0.425 | AGFAGDDAPR | n.d. | |||||
| 0.123 | 0.760 | AGFAGDDAPRAVFPSIVGRP | ||||||
| 0.162 | 1.044 | AGFAGDDAPRAVFPSIVGRPR | ||||||
| 1.038 | −2.015 | GQKDSYVGDEAQSK | n.d. | |||||
| 1.439 | −0.739 | HQGVMVGMGQKDSYVGDEAQSK | ||||||
| 0.285 | −1.180 | IVGRPRHQGVMVGMGQKDSYVGDEAQSK | ||||||
| 0.412 | 1.787 | MGQKDSYVGDEAQSK | ||||||
| 0.218 | −0.128 | DSYVGDEAQSK | ||||||
| 0.403 | −1.718 | SYELPDGQVITIGNER | n.d. | |||||
| 0.000 | 0.000 | SYELPDGQVITIGNERF | ||||||
| 0.761 | 3.078 | SYELPDGQVITIGNERFR | ||||||
| 0.272 | −1.106 | MQKEITALAPSTMK | n.d. | |||||
| 0.541 | −0.306 | EITALAPSTMK | ||||||
| 0.083 | −0.418 | DLYANTVLSGGTTMYPGIADR | n.d. | |||||
| 0.053 | −0.476 | EIVRDIKEKL | n.d. | |||||
| 0.936 | 4.532 | VAPEEHPVLLTEAPLNPK | n.d. | |||||
| 1.921 | 5.279 | LNTILPDARD |
P11279 LAMP1 |
+ | 4.065 | 1.838 | LNTILPDARDPAFK | |
| 0.155 | 0.853 | LNTILPDARDPAF | ||||||
| 0.028 | 0.039 | LNTILPDARDPAFK | ||||||
| 1.909 | 5.834 | LNTILPDARDPAFKA | ||||||
| 0.276 | 1.433 | QLNTILPDARDPAFK | ||||||
Comparison of the log2-fold change enrichment (DMH-DML) and the corresponding −log(P-values) for each peptide (left) or epitope (right) of three protein entries with highly abundant peptides. Uniprot accession codes of the protein sources are indicated as well as the original sequence of the peptides and the corresponding epitope provided by peptide landscape antigenic epitope alignment utility (PLAtEAU).
Diff. stands for the difference of the log2-transformed intensity values and the −log(P-value) was estimated using a t-test considering all samples for each condition.
n.d. stands for not determined, in most of the cases peptides did not pass either the replication filter (two out of three replicates), the removal of background binders or any of them.