Date: 2021-09-22
Submitted by: Isabelle Sirois
Analysis type: Class I
MHC CLASS I MOUSE EL4 USER2 - 3 BIOLOGICAL REPLICATES
MHC1_EL4_USER2_N1: Alleles: H-2-Kb, H-2-Db MHC1_EL4_USER2_N2: Alleles: H-2-Kb, H-2-Db MHC1_EL4_USER2_N3: Alleles: H-2-Kb, H-2-Db
Species: MOUSE - EL4
# of cells: 100 M
Lysis buffer: 0.5% CHAPS
Type of beads: 80 mg Sepharose CNBr-activated beads
Antibody: M1 pan H2
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 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 |
---|---|---|---|---|
MHC1_EL4_USER2_N1 | 1723 | 1645 | 0.95 | 0.83 |
MHC1_EL4_USER2_N2 | 1767 | 1679 | 0.95 | 0.89 |
MHC1_EL4_USER2_N3 | 1846 | 1745 | 0.95 | 0.88 |
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 |
---|---|---|---|---|---|
MHC1_EL4_USER2_N1 |
1645 | H-2-Kb | 743 (45.2%) | 227 (13.8%) | 675 (41.0%) |
H-2-Db | 603 (36.7%) | 203 (12.3%) | 839 (51.0%) | ||
MHC1_EL4_USER2_N2 |
1679 | H-2-Kb | 936 (55.7%) | 236 (14.1%) | 507 (30.2%) |
H-2-Db | 508 (30.3%) | 233 (13.9%) | 938 (55.9%) | ||
MHC1_EL4_USER2_N3 |
1745 | H-2-Kb | 981 (56.2%) | 237 (13.6%) | 527 (30.2%) |
H-2-Db | 534 (30.6%) | 246 (14.1%) | 965 (55.3%) |
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
MHC1_EL4_USER2_N1 (peptides clustered: 1645, outliers: 16)
Peptides in group: 202
H-2-Kb: 13%,
H-2-Db: 18%Peptides in group: 448
H-2-Db: 6%
Peptides in group: 114
H-2-Kb: 0%,
H-2-Db: 0%
Peptides in group: 330
H-2-Db: 10%
Peptides in group: 535
H-2-Kb: 9%,
H-2-Db: 95%MHC1_EL4_USER2_N2 (peptides clustered: 1679, outliers: 19)
Peptides in group: 782
H-2-Db: 4%
Peptides in group: 431
H-2-Kb: 11%,
H-2-Db: 94%Peptides in group: 221
H-2-Db: 11%
Peptides in group: 226
H-2-Kb: 16%,
H-2-Db: 19%MHC1_EL4_USER2_N3 (peptides clustered: 1745, outliers: 46)
Peptides in group: 248
H-2-Kb: 13%,
H-2-Db: 16%Peptides in group: 986
H-2-Db: 7%
Peptides in group: 465
H-2-Kb: 12%,
H-2-Db: 92%Peptides: 964
Peptides: 796
Peptides: 126
Peptides: 128
Peptides: 1161
Peptides: 736
Peptides: 65
Peptides: 114
Peptides: 1208
Peptides: 777
Peptides: 134
Peptides: 57