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- 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