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@ARTICLE{CosenzaContreras:305000,
      author       = {M. Cosenza-Contreras and P. F. Huesgen and O.
                      Schilling$^*$},
      title        = {{T}ermine{R}: {B}ioinformatic processing of shotgun
                      proteomics data for the annotation and quantitation of
                      protein termini.},
      journal      = {Methods in enzymology},
      volume       = {719},
      issn         = {0076-6879},
      address      = {New York, NY [u.a.]},
      publisher    = {Elsevier},
      reportid     = {DKFZ-2025-01991},
      pages        = {43-66},
      year         = {2025},
      abstract     = {Proteolytic processing shapes protein function through
                      irreversible cleavage events that are often overlooked in
                      standard shotgun proteomics workflows. In this methods
                      chapter, we describe a comprehensive strategy for the
                      identification, annotation, and quantitation of proteolytic
                      products and terminal peptides using semi-specific database
                      searches. We present practical guidelines for spectral data
                      processing using the FragPipe software suite, leveraging
                      modern rescoring tools such as Percolator and MSBooster to
                      improve sensitivity. Building upon this, we introduce
                      TermineR, an R-based framework for downstream annotation and
                      statistical evaluation of proteolytic termini. Together,
                      these tools enable the extraction of biologically meaningful
                      insights into proteolytic activity from complex proteomics
                      datasets, without the need for biochemical enrichment.},
      keywords     = {Proteomics: methods / Software / Databases, Protein /
                      Computational Biology: methods / Proteolysis / Proteins:
                      chemistry / Proteins: metabolism / Molecular Sequence
                      Annotation: methods / Peptides: analysis / Peptides:
                      chemistry / Humans / Tandem Mass Spectrometry: methods /
                      Bioinformatics (Other) / Data Processing (Other) /
                      Degradomics (Other) / N-terminomics (Other) /
                      Post-translational modifications (Other) / Proteolysis
                      (Other) / Proteomics (Other) / Terminomics (Other) /
                      Proteins (NLM Chemicals) / Peptides (NLM Chemicals)},
      cin          = {FR01},
      ddc          = {570},
      cid          = {I:(DE-He78)FR01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40992848},
      doi          = {DOI:10.1016/bs.mie.2025.06.004},
      url          = {https://inrepo02.dkfz.de/record/305000},
}