% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@ARTICLE{Demir:891164,
      author       = {Demir, Fatih and Kizhakkedathu, Jayachandran N. and
                      Rinschen, Markus M. and Huesgen, Pitter F.},
      title        = {{MANTI}: {A}utomated {A}nnotation of {P}rotein
                      {N}-{T}ermini for {R}apid {I}nterpretation of
                      {N}-{T}erminome {D}ata {S}ets},
      journal      = {Analytical chemistry},
      volume       = {93},
      number       = {13},
      issn         = {1520-6882},
      address      = {Columbus, Ohio},
      publisher    = {American Chemical Society},
      reportid     = {FZJ-2021-01402},
      pages        = {5596–5605},
      year         = {2021},
      abstract     = {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.},
      cin          = {ZEA-3},
      ddc          = {540},
      cid          = {I:(DE-Juel1)ZEA-3-20090406},
      pnm          = {217 - Für eine nachhaltige Bio-Ökonomie – von
                      Ressourcen zu Produkten (POF4-217) / ProPlantStress -
                      Proteolytic processing in plant stress signal transduction
                      and responses to abiotic stress and pathogen attack
                      (639905)},
      pid          = {G:(DE-HGF)POF4-217 / G:(EU-Grant)639905},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {33729755},
      UT           = {WOS:000638986400032},
      doi          = {10.1021/acs.analchem.1c00310},
      url          = {https://juser.fz-juelich.de/record/891164},
}