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- Analysis report


Date: 2021-09-22

Submitted by: Isabelle Sirois

Analysis type: Class I

Description of experiment:

MHC CLASS I HUMAN JY USER2 - 3 BIOLOGICAL REPLICATES

Samples:

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%


Sample Overview

- 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
UpSet Plot (only displaying intersections containing >= 1% of at least one sample)

Peptide Length Distribution (maximum of 30 mers)


Annotation Results

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%)
Binding Affinities

Binding Heatmaps

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


Sequence Motifs

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-A0201: 85%,

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-A0201: 87%,

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-A0201: 88%,

HLA-B0702: 0%,

HLA-C0702: 15%

MHCI_JY_USER2_N1 sequence motif(s)
HLA-A0201

Peptides: 2157

HLA-B0702

Peptides: 4370

HLA-C0702

Peptides: 1955

Non-binders group 2

Peptides: 147

Non-binders group 1

Peptides: 119

MHCI_JY_USER2_N2 sequence motif(s)
HLA-A0201

Peptides: 2586

HLA-B0702

Peptides: 3729

HLA-C0702

Peptides: 2077

Non-binders group 1

Peptides: 186

MHCI_JY_USER2_N3 sequence motif(s)
HLA-A0201

Peptides: 2657

HLA-B0702

Peptides: 3631

HLA-C0702

Peptides: 2101

Non-binders group 2

Peptides: 74

Non-binders group 1

Peptides: 122