TABLE II.
Identification and quantification of the Ii-chain peptides bound to DQ2 and DR3. (A) Peptides acid-eluted from 50 μg of affinity-purified DQ2 and DR3 from 8.1.6 and 9.5.3 B-LCLs were sequenced using LC-coupled ESI-MS/MS to identify all Ii-chain peptide truncations present in at least one of the elutions. The peptides were present in multiple charged states (2–5 fold) and the observed molecular weight (MW) was calculated by deconvolution. (B) The quantities of the individual Ii-chain peptides as listed above are given, and the data have been summarized in Fig. 3. ND= not detected, na=not applicable.
| A | |||||||
|---|---|---|---|---|---|---|---|
| Residues | Sequence | Detected | Length | MW | |||
| DQ2DM+ | DQ2DM− | DR3DM+ | DR3DM− | ||||
| Ii81-104 | LPKPPKPVSKMRMATPLLMQALPM | − | − | − | + | 24 | 2674.5 |
| Ii81-103 | LPKPPKPVSKMRMATPLLMQALP | + | + | + | + | 23 | 2543.4 |
| Ii82-103 | PKPPKPVSKMRMATPLLMQALP | + | + | − | + | 22 | 2430.4 |
| Ii81-101 | LPKPPKPVSKMRMATPLLMQA | + | + | − | + | 21 | 2333.3 |
| Ii93-109 | MATPLLMQALPMGALPQ | + | + | − | − | 17 | 1781.9 |
| Ii93-108 | MATPLLMQALPMGALP | + | + | − | − | 16 | 1653.9 |
| B | |||
|---|---|---|---|
| MHC II | Peptide | pmol | SD |
| DQ2 (8.1.6) | Ii81-104 | ND | na |
| Ii81-103 | 79,5 | 31,8 | |
| Ii82-103 | 16,5 | 9,5 | |
| Ii81-101 | 31,5 | 3,2 | |
| Ii93-109 | ND | na | |
| Ii93-108 | 159,0 | 1,1 | |
| DQ2 (9.5.3) | Ii81-104 | ND | na |
| Ii81-103 | 71,1* | 29,2 | |
| Ii82-103 | 36,8* | 14,5 | |
| Ii81-101 | 88,4* | 35,6 | |
| Ii93-109 | 3,8 | 6,5 | |
| Ii93-108 | 156,3 | 62,6 | |
| DR3 (8.1.6) | Ii81-104 | ND | na |
| Ii81-103 | 14,9 | 19,7 | |
| Ii82-103 | ND | na | |
| Ii81-101 | ND | na | |
| Ii93-109 | ND | na | |
| Ii93-108 | ND | na | |
| DR3 (9.5.3) | Ii81-104 | 42,4 | 3,7 |
| Ii81-103 | 128,3* | 23,3 | |
| Ii82-103 | 113,3 | 22,3 | |
| Ii81-101 | 106,1 | 8,0 | |
| Ii93-109 | ND | na | |
| Ii93-108 | ND | na | |
Underestimated due to suboptimal ICPL labeling of eluted peptides from 9.5.3 cells. A rough estimation indicate that about 3% and 8% percent of total CLIP peptides remained unlabeled when eluted from DQ2 and DR3, respectively.