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RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control.
Kurt, Louise Ulrich; Clasen, Milan Avila; Biembengut, Ísis Venturi; Ruwolt, Max; Liu, Fan; Gozzo, Fabio César; Lima, Diogo Borges; Carvalho, Paulo Costa.
Afiliação
  • Kurt LU; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil.
  • Clasen MA; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil.
  • Biembengut ÍV; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil.
  • Ruwolt M; Department of Chemical Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany.
  • Liu F; Department of Chemical Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany.
  • Gozzo FC; Dalton Mass Spectrometry Laboratory, Unicamp, Campinas, Sao Paulo 13083-970, Brazil.
  • Lima DB; Department of Chemical Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany.
  • Carvalho PC; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil.
J Proteome Res ; 23(8): 3141-3148, 2024 Aug 02.
Article em En | MEDLINE | ID: mdl-38301217
ABSTRACT
We present RawVegetable 2.0, a software tailored for assessing mass spectrometry data quality and fine-tuned for cross-linking mass spectrometry (XL-MS) applications. Building upon the capabilities of its predecessor, RawVegetable 2.0 introduces four main modules, each providing distinct and new functionalities 1) Pair Finder, which identifies ion doublets characteristic of cleavable cross-linking experiments; 2) Diagnostic Peak Finder, which locates potential reporter ions associated with a specific cross-linker; 3) Precursor Signal Ratio, which computes the ratio between precursor intensity and the total signal in an MS/MS scan; and 4) Xrea, which evaluates spectral quality by analyzing the heterogeneity of peak intensities within a spectrum. These modules collectively streamline the process of optimizing mass spectrometry data acquisition for both Proteomics and XL-MS experiments. RawVegetable 2.0, along with a comprehensive tutorial is freely accessible for academic use at http//patternlabforproteomics.org/rawvegetable2.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Controle de Qualidade / Software / Proteômica / Espectrometria de Massas em Tandem Tipo de estudo: Prognostic_studies Idioma: En Revista: J Proteome Res Assunto da revista: BIOQUIMICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil País de publicação: Estados Unidos
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Controle de Qualidade / Software / Proteômica / Espectrometria de Massas em Tandem Tipo de estudo: Prognostic_studies Idioma: En Revista: J Proteome Res Assunto da revista: BIOQUIMICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil País de publicação: Estados Unidos