Table 3.
Enrichment behavior of peptides and epitopes of three abundant protein entries.
| MaxQuant-peptides | Uniprot accession | PLAtEAU-epitopes | ||||||
|---|---|---|---|---|---|---|---|---|
| Sig. | −log(P) | Diff. | Sequence | Sig. | −log(P) | Diff. | Sequence | |
| 0.608 | −1.124 | KSWITFDLKNKE |
P01730 CD4 |
+ | 4.042 | −1.134 | KSWITFDLKNKE* | |
| 1.096 | −2.279 | KSWITFDLKNKEV | ||||||
| 2.360 | −1.443 | KSWITFDLKNKEVS | ||||||
| 1.259 | −1.705 | KSWITFDLKNKEVSV | ||||||
| 2.162 | −2.503 | KSWITFDLKNKEVSVK | ||||||
| 0.170 | −1.086 | RASSSKSWITFDLKNKEVSVK | ||||||
| 0.414 | −1.178 | SKSWITFDLKNKE | ||||||
| 0.070 | −0.675 | SKSWITFDLKNKEV | ||||||
| 2.935 | −1.241 | SKSWITFDLKNKEVS | ||||||
| 0.825 | −2.376 | SKSWITFDLKNKEVSV | ||||||
| 1.420 | −2.279 | SKSWITFDLKNKEVSVK | ||||||
| 0.182 | 0.729 | SSKSWITFDLKNKE | ||||||
| 0.005 | −0.038 | SSKSWITFDLKNKEV | ||||||
| 1.897 | −1.375 | SSKSWITFDLKNKEVS | ||||||
| 0.906 | −3.922 | SSKSWITFDLKNKEVSVK | ||||||
| 0.495 | 1.496 | SVKRVTQDPKLQMGKK | n.d. | |||||
| 0.160 | −0.912 | VKRVTQDPKLQMGKK | 0.004 | −0.022 | *VKRVTQDPKLQMGKK | |||
| + | 7.711 | −6.558 | EDQKPVMDDQRDLISNN |
P04233 CD74 |
+ | 7.563 | −7.223 | EDQKPVMDDQRDLISNN |
| 1.684 | −5.471 | EDQKPVMDDQRDLISNNE | ||||||
| 0.098 | −0.605 | APPKESLELEDPSSGLGVTKQDLGPVPM | 0 | 0 | APPKESLELEDPSSGLGVTKQDLGPVPM | |||
| + | 6.307 | −9.676 | KPVSKMRMATPLLMQALP | + | 5.263 | −4.609 | KPVSKMRMATPLLMQA | |
| 1.406 | −1.669 | KPPKPVSKMRMATPLLMQA | ||||||
| 0.778 | −3.627 | KPPKPVSKMRMATPLLMQAL | ||||||
| 2.028 | −3.301 | KPPKPVSKMRMATPLLMQALP | ||||||
| 2.374 | −5.947 | KPPKPVSKMRMATPLLMQALPM | ||||||
| 1.634 | −4.517 | KPVSKMRMATPLLMQA | ||||||
| 3.555 | −3.864 | KPVSKMRMATPLLMQAL | ||||||
| 0.000 | 0.000 | LPKPPKPVSKMRMATPLLMQAL | ||||||
| 1.214 | −7.773 | LPKPPKPVSKMRMATPLLMQALPM | ||||||
| 0.836 | −2.487 | RMATPLLMQALPM | ||||||
| 0.000 | 0.000 | MKLPKPPKPVSKMR | n.d. | |||||
| 0.488 | −0.583 | PSSGLGVTKQDLGPVPM | n.d. | |||||
| 0.980 | 3.583 | LTVTSQNLQLENLR | n.d. | |||||
| 0.415 | 1.473 | DVKIYLDENYERIN |
Q9NQX7 Integral membrane protein 2 |
+ | 3.418 | 1.449 | KIYLDENYERIN | |
| 0.000 | 0.000 | DVKIYLDENYERINV | ||||||
| 0.196 | 1.133 | DVKIYLDENYERINVP | ||||||
| 0.837 | −0.961 | EDVKIYLDENYERIN | ||||||
| 0.379 | 1.918 | EDVKIYLDENYERINV | ||||||
| 0.428 | −3.087 | EDVKIYLDENYERINVP | ||||||
| 0.702 | 1.292 | EDVKIYLDENYERINVPV | ||||||
| 0.814 | 3.644 | EDVKIYLDENYERINVPVP | ||||||
| 0.035 | −0.092 | EDVKIYLDENYERINVPVPQ | ||||||
| 0.209 | −1.055 | EDVKIYLDENYERINVPVPQFG | ||||||
| 0.600 | 3.035 | EEDVKIYLDENYERIN | ||||||
| 0.835 | 2.703 | EEDVKIYLDENYERINVP | ||||||
| 1.175 | 4.143 | EEDVKIYLDENYERINVPV | ||||||
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.
Asterisks (*) indicates that the epitope arises from the overlap of two potential register-shifted epitopes and indicates the position (N- or C-terminal) of the “jump” (see Figure 1).