OUTPUT EXAMPLE

FASTA

>ENSP00000253039.4 TPM=80.3919983
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPE

Peptide length: 8, 9, 10, 11

Input format: TPM values given in the input file

Allele: HLA-A*0201

Threshold for strong binder: 0.5 %Rank

Threshold for weak binder: 2.0 %Rank

Filtering threshold for %Rank: -99

Sort by prediction score: On

Exclude Expression in prediction: Off

Define MAX TPM capping value: 10000


# NetMHCpanExp version 1.0

# Tmpdir made /var/www/webface/tmp/server/netmhcpanexp/6237B40000005ED4FDF6B89C/netMHCpanv9J7VL
# Input is in FSA format

# Peptide length 8,9,10,11

# Make predictions including expression

HLA-A02:01 : Distance to training data  0.000 (using nearest neighbor HLA-A02:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
------------------------------------------------------------------------------------------------------------
 Pos         HLA        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL  Rnk_EL      Exp BindLevel
------------------------------------------------------------------------------------------------------------
  27 HLA-A*02:01      KLTPLSHEV KLTPLSHEV  0  0  0  0  0    KLTPLSHEV ENSP00000253039 0.9951022   0.009  0.47764 <= SB
  59 HLA-A*02:01      KAISGVHTV KAISGVHTV  0  0  0  0  0    KAISGVHTV ENSP00000253039 0.9754907   0.074  0.47764 <= SB
  83 HLA-A*02:01      YANAKIYKL YANAKIYKL  0  0  0  0  0    YANAKIYKL ENSP00000253039 0.9058493   0.237  0.47764 <= SB
  56 HLA-A*02:01      TVVKAISGV TVVKAISGV  0  0  0  0  0    TVVKAISGV ENSP00000253039 0.7207928   0.635  0.47764 <= WB
  57 HLA-A*02:01    VVKAISGVHTV VVISGVHTV  0  2  2  0  0  VVKAISGVHTV ENSP00000253039 0.6767913   0.746  0.47764 <= WB
  25 HLA-A*02:01    VTKLTPLSHEV VLTPLSHEV  0  1  2  0  0  VTKLTPLSHEV ENSP00000253039 0.6566866   0.793  0.47764 <= WB
  26 HLA-A*02:01     TKLTPLSHEV TLTPLSHEV  0  1  1  0  0   TKLTPLSHEV ENSP00000253039 0.5708980   0.988  0.47764 <= WB
  27 HLA-A*02:01     KLTPLSHEVI KLTPLSHEI  0  8  1  0  0   KLTPLSHEVI ENSP00000253039 0.5401132   1.077  0.47764 <= WB
  80 HLA-A*02:01      KLGYANAKI KLGYANAKI  0  0  0  0  0    KLGYANAKI ENSP00000253039 0.4893585   1.206  0.47764 <= WB
  14 HLA-A*02:01     HLSRQDLTTL HLSQDLTTL  0  3  1  0  0   HLSRQDLTTL ENSP00000253039 0.4232187   1.430  0.47764 <= WB
  60 HLA-A*02:01       AISGVHTV AI-SGVHTV  0  0  0  2  1     AISGVHTV ENSP00000253039 0.3835837   1.575  0.47764 <= WB
  22 HLA-A*02:01     TLDVTKLTPL TLDVTKLTL  0  8  1  0  0   TLDVTKLTPL ENSP00000253039 0.3285049   1.809  0.47764 <= WB
  58 HLA-A*02:01     VKAISGVHTV VAISGVHTV  0  1  1  0  0   VKAISGVHTV ENSP00000253039 0.2115432   2.467  0.47764
  55 HLA-A*02:01     STVVKAISGV SVVKAISGV  0  1  1  0  0   STVVKAISGV ENSP00000253039 0.1888403   2.654  0.47764
  40 HLA-A*02:01    ATINIGTIGHV ATINIGTHV  0  7  2  0  0  ATINIGTIGHV ENSP00000253039 0.1826325   2.710  0.47764

DESCRIPTION

The prediction output consists of the following columns:

Pos: Residue number (starting from 0) of the peptide in the protein sequence (if the input is in peptide format, dismiss this column).

HLA: Specified MHC molecule / Allele name.

Peptide: Amino acid sequence of the potential ligand.

Core: The minimal 9 amino acid binding core directly in contact with the MHC.

Of: The starting position of the Core within the Peptide (if > 0, the method predicts a N-terminal protrusion).

Gp: Position of the deletion, if any.

Gl: Length of the deletion, if any.

Ip: Position of the insertion, if any.

Il: Length of the insertion, if any.

Icore: Interaction core. This is the sequence of the binding core including eventual insertions of deletions.

Identity: Protein identifier, i.e. the name of the FASTA entry.

Score: The raw prediction score.

%Rank: Rank of the predicted binding score compared to a set of random natural peptides for the corresponding MHC molecule. This measure is not affected by the inherent bias of certain molecules towards higher or lower mean predicted scores. We advise to select candidate binders based on %Rank rather than Score.

Exp: The gene expression value in TPM normalized by the maximum TPM value specified by the user (default: 10000 TPM). If the expression values were excluded from the prediction, this column will not appear in the output.

BindLevel: (SB: Strong Binder, WB: Weak Binder). The peptide will be identified as a strong binder if the %Rank is below the specified threshold for the strong binders (default: 0.5%). The peptide will be identified as a weak binder if the %Rank is above the threshold of the strong binders but below the specified threshold for the weak binders (default: 2%).

NOTES

Peptide vs. iCore vs. Core

Three amino acid sequences are reported for each peptide (row) in the prediction output:

The Peptide is the complete amino acid sequence evaluated by NetMHCpanExp. Peptides are the full sequences submitted as a peptide list, or the result of the digestion of source proteins (submission in FASTA format)

The iCore is a substring of Peptide, encompassing all residues between P1 and P-omega interacting with the MHC. For all intents and purposes, this is the minimal candidate ligand that should be considered for further validation.

The Core is always 9 amino acids long and is a construction used for sequence alignment and identification of binding anchors.