Date: 2021-09-22
Submitted by: Isabelle Sirois
Analysis type: Class I
MHC CLASS I HUMAN JY USER2 - 3 BIOLOGICAL REPLICATES
MHCI_JY_USER2_N1: Alleles: HLA-A0201, HLA-B0702, HLA-C0702 MHCI_JY_USER2_N2: Alleles: HLA-A0201, HLA-B0702, HLA-C0702 MHCI_JY_USER2_N3: Alleles: HLA-A0201, HLA-B0702, HLA-C0702
Species: HUMAN - JY
# of cells: 100 M
Lysis buffer: 0.5% CHAPS
Type of beads: 80 mg Sepharose CNBr-activated beads
Antibody: W6/32 Pan HLA-ABC
Incubation time: overnight
MHC-ligand complex elution buffer: 1% TFA
Peptide elution buffer: 28% ACN/0.1%TFA
Type of MS/MS: ORBITRAP ECLIPSE TRIBID MASS SPECTROMETER
Peptide identification software: PEAKS PRO V10.6
Peptide FDR: 1%
- LF Score: fraction of peptides between 8 and 12 mers. - BF Score: fraction of peptides between 8 and 12 mers which are predicted to be strong or weak binders.
Sample | Total peptides | Peptides between 8-12 mers | LF Score | BF Score |
---|---|---|---|---|
MHCI_JY_USER2_N1 | 6986 | 6705 | 0.96 | 0.95 |
MHCI_JY_USER2_N2 | 6793 | 6476 | 0.95 | 0.96 |
MHCI_JY_USER2_N3 | 6794 | 6430 | 0.95 | 0.96 |
Peptide Length Distribution (maximum of 30 mers)
NetMHCpan eluted ligand predictions made for all peptides between 8 & 12 mers, inclusive. - Percent rank cutoffs for strong and weak binders: 0.5 and 2.0. - Percentages are calculated across rows (i.e. percentage of total peptides for a respective sample).
Sample | Total peptides | Allele | Strong binders | Weak binders | Non-binders |
---|---|---|---|---|---|
MHCI_JY_USER2_N1 |
6705 | HLA-A0201 | 1918 (28.6%) | 252 (3.8%) | 4535 (67.6%) |
HLA-B0702 | 3839 (57.3%) | 563 (8.4%) | 2303 (34.3%) | ||
HLA-C0702 | 456 (6.8%) | 1554 (23.2%) | 4695 (70.0%) | ||
MHCI_JY_USER2_N2 |
6476 | HLA-A0201 | 2320 (35.8%) | 291 (4.5%) | 3865 (59.7%) |
HLA-B0702 | 3241 (50.0%) | 513 (7.9%) | 2722 (42.0%) | ||
HLA-C0702 | 576 (8.9%) | 1545 (23.9%) | 4355 (67.2%) | ||
MHCI_JY_USER2_N3 |
6430 | HLA-A0201 | 2404 (37.4%) | 282 (4.4%) | 3744 (58.2%) |
HLA-B0702 | 3182 (49.5%) | 478 (7.4%) | 2770 (43.1%) | ||
HLA-C0702 | 586 (9.1%) | 1553 (24.2%) | 4291 (66.7%) |
NetMHCpan eluted ligand predictions made for all peptides between 8 & 12 mers, inclusive. Approximate color legend (detailed mapping shown next to heatmaps):
Predicted strong binders (%rank <= 0.5)
Predicted weak binders (0.5 < %rank <= 2.0)
Predicted non-binders
- - # of peptides in sample
Clustering performed with all peptides between 8 & 12 mers, inclusive.
- Percentages represent the percentage of peptides in a given group predicted to strongly bind the indicated allele.
Polar
Neutral
Basic
Acidic
Hydrophobic
MHCI_JY_USER2_N1 (peptides clustered: 6705, outliers: 196)
Peptides in group: 4271
HLA-A0201: 0%,
HLA-B0702: 89%,HLA-C0702: 3%
Peptides in group: 2238
HLA-B0702: 2%,
HLA-C0702: 12%
MHCI_JY_USER2_N2 (peptides clustered: 6476, outliers: 176)
Peptides in group: 3646
HLA-A0201: 0%,
HLA-B0702: 88%,HLA-C0702: 3%
Peptides in group: 2654
HLA-B0702: 1%,
HLA-C0702: 15%
MHCI_JY_USER2_N3 (peptides clustered: 6430, outliers: 201)
Peptides in group: 3519
HLA-A0201: 0%,
HLA-B0702: 90%,HLA-C0702: 3%
Peptides in group: 2710
HLA-B0702: 0%,
HLA-C0702: 15%
Peptides: 2157
Peptides: 4370
Peptides: 1955
Peptides: 147
Peptides: 119
Peptides: 2586
Peptides: 3729
Peptides: 2077
Peptides: 186
Peptides: 2657
Peptides: 3631
Peptides: 2101
Peptides: 74
Peptides: 122