Date: 2021-09-22
Submitted by: Isabelle Sirois
Analysis type: Class II
MHC CLASS II MOUSE A20
MHC_CLASS_II_FROM_MOUSE_A20_CELLS_-_M5_ANTIBODY: Alleles: H-2-IAd, H-2-IEd
Species: MOUSE A20
# of cells: 100 M
Lysis buffer: 0.5 % CHAPS
Type of beads: 80 mg Sepharose CNBr-activated beads
Antibody: M5 - H2 IAd/IEd - 2 MG
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 9 and 22 mers. - BF Score: fraction of peptides between 9 and 22 mers which are predicted to be strong or weak binders.
Sample | Total peptides | Peptides between 9-22 mers | LF Score | BF Score |
---|---|---|---|---|
MHC_CLASS_II_FROM_MOUSE_A20_CELLS_-_M5_ANTIBODY | 2295 | 2219 | 0.97 | 0.87 |
Peptide Length Distribution (maximum of 30 mers)
NetMHCIIpan eluted ligand predictions made for all peptides between 9 & 22 mers, inclusive. - Percent rank cutoffs for strong and weak binders: 2.0 and 10.0. - 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 |
---|---|---|---|---|---|
MHC_CLASS_II_FROM_MOUSE_A20_CELLS_-_M5_ANTIBODY |
2219 | H-2-IAd | 956 (43.1%) | 338 (15.2%) | 925 (41.7%) |
H-2-IEd | 556 (25.1%) | 514 (23.2%) | 1149 (51.8%) |
NetMHCIIpan eluted ligand predictions made for all peptides between 9 & 22 mers, inclusive. Approximate color legend (detailed mapping shown next to heatmaps):
Predicted strong binders (%rank <= 2.0)
Predicted weak binders (2.0 < %rank <= 10.0)
Predicted non-binders
- - # of peptides in sample
Clustering performed with all peptides between 9 & 22 mers, inclusive.
- Percentages represent the percentage of peptides in a given group predicted to strongly bind the indicated allele.
Polar
Neutral
Basic
Acidic
Hydrophobic
MHC_CLASS_II_FROM_MOUSE_A20_CELLS_-_M5_ANTIBODY (peptides clustered: 2219, outliers: 101)
Peptides in group: 792
H-2-IAd: 6%,
H-2-IEd: 55%Peptides in group: 1326
H-2-IEd: 9%
Peptides: 1277
Peptides: 1046
Peptides: 140
Peptides: 116