MANTI: Automated Annotation of Protein N‑Termini for Rapid Interpretation of N‑Terminome Data Sets

Site-specific proteolytic
processing is an important, irreversible
post-translational protein modification with implications in many
diseases. Enrichment of protein N-terminal peptides followed by mass
spectrometry-based identification and quantification enables proteome-wide
characterization of proteolytic processes and protease substrates
but is challenged by the lack of specific annotation tools. A common
problem is, for example, ambiguous matches of identified peptides
to multiple protein entries in the databases used for identification.
We developed MaxQuant Advanced N-termini Interpreter (MANTI), a standalone
Perl software with an optional graphical user interface that validates
and annotates N-terminal peptides identified by database searches
with the popular MaxQuant software package by integrating information
from multiple data sources. MANTI utilizes diverse annotation information
in a multistep decision process to assign a conservative preferred
protein entry for each N-terminal peptide, enabling automated classification
according to the likely origin and determines significant changes
in N-terminal peptide abundance. Auxiliary R scripts included in the
software package summarize and visualize key aspects of the data.
To showcase the utility of MANTI, we generated two large-scale TAILS
N-terminome data sets from two different animal models of chemically
and genetically induced kidney disease, puromycin adenonucleoside-treated
rats (PAN), and heterozygous Wilms Tumor protein 1 mice (WT1). MANTI
enabled rapid validation and autonomous annotation of >10 000
identified terminal peptides, revealing novel proteolytic proteoforms
in 905 and 644 proteins, respectively. Quantitative analysis indicated
that proteolytic activities with similar sequence specificity are
involved in the pathogenesis of kidney injury and proteinuria in both
models, whereas coagulation processes and complement activation were
specifically induced after chemical injury.