PRBAM: a new tool to analyze the MHC class I and HLA-DR anchor motifs

Anna Mestre Ferrer, Erika Margaret Scholz Valero, Jepi Humet-Alsius, Ignacio Gerardo Alvarez Perez*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review


Major histocompatibility complex (MHC) genes are highly polymorphic,
which makes each MHC molecule different regarding their peptide repertoire,
so they can bind and present to T lymphocytes. The increasing
importance of immunopeptidomics and its use in personalized medicine
in different fields such as oncology or autoimmunity demand the correct
analysis of the peptide repertoires bound to human leukocyte antigen type
1 (HLA-I) and HLA-II molecules. Purification of the peptide pool by
affinity chromatography and individual peptide sequencing using mass
spectrometry techniques is the standard protocol to define the binding
motifs of the different MHC-I and MHC-II molecules. The identification
of MHC-I binding motifs is relatively simple, but it is more complicated
for MHC-II. There are some programs that identify the anchor motifs of
MHC-II molecules. However, these programs do not identify the anchor
motif correctly for some HLA-II molecules and some anchor motifs have
been deduced using subjective interpretation of the data. Here, we present
a new software, called PRBAM (Peptide Repertoire-Based Anchor Motif)
that uses a new algorithm based on the peptide–MHC interactions and,
using peptide lists obtained by mass spectrometry sequencing, identifies
the binding motif of MHC-I and HLA-DR molecules. PRBAM has an
easy-to-use interface, and the results are presented in graphics, tables and
peptide lists. Finally, the fact that PRBAM uses a new algorithm makes it
complementary to other existing programs.
Original languageEnglish
Pages (from-to)187
Number of pages198
Publication statusPublished - 2019

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