# M

### hc

# V

### iz

# P

### ipe

##### (v0.7.8)

### - Analysis report

Date: 2021-09-22

Submitted by: Isabelle Sirois

Analysis type: Class II

Description of experiment:

MHC CLASS II HUMAN JY

Samples:

MHC_CLASS_II_FROM_JY_-_L243_ANTIBODY: Alleles: DRB1_0404, DRB1_1301

Species: HUMAN - JY

# of cells: 100 M

Lysis buffer: 0.5% CHAPS

Type of beads: 80 mg Sepharose CNBr-activated beads

Antibody: L243 - 2 mg

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%

### Sample Overview

- 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_JY_-_L243_ANTIBODY | 1707 | 1614 | 0.95 | 0.7

Peptide Length Distribution (maximum of 30 mers)

### Annotation Results

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_JY_-_L243_ANTIBODY | 1614 | DRB1_0404 | 627 (38.8%) | 352 (21.8%) | 635 (39.3%)
DRB1_1301 | 125 (7.7%) | 338 (20.9%) | 1151 (71.3%)

Binding Affinities

### Binding Heatmaps

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

### Sequence Motifs

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_JY_-_L243_ANTIBODY (peptides clustered: 1614, outliers: 36)

Peptides in group: 270

DRB1_0404: 11%,

DRB1_1301: 20%

Peptides in group: 603

DRB1_0404: 63%,

DRB1_1301: 8%

Peptides in group: 265

DRB1_0404: 35%,

DRB1_1301: 7%

Peptides in group: 440

DRB1_0404: 29%,

DRB1_1301: 1%

MHC_CLASS_II_FROM_JY_-_L243_ANTIBODY sequence motif(s)
DRB1_0404

Peptides: 966

DRB1_1301

Peptides: 447

Non-binders group 2

Peptides: 246

Non-binders group 1

Peptides: 202