| Author | Kurt, Louise Ulrich | |
| Author | Clasen, Milan Avila | |
| Author | Biembengut, Isís Venturi | |
| Author | Ruwolt, Max | |
| Author | Liu, Fan | |
| Author | Gozzo, Fabio César | |
| Author | Lima, Diogo Borges | |
| Author | Carvalho, Paulo Costa | |
| Access date | 2024-02-28T16:30:03Z | |
| Available date | 2024-02-28T16:30:03Z | |
| Document date | 2024 | |
| Citation | KURT, Louise Ulrich et al. RawVegetable 2.0: Refining XL-MS data acquisition through enhanced quality control. J. Proteome Res., p. [1-8], 2024. | en_US |
| ISSN | 1535-3907 | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/62828 | |
| Language | por | en_US |
| Publisher | American Chemical Society | en_US |
| Rights | open access | en_US |
| Subject in Portuguese | Bioinformática | en_US |
| Title | RawVegetable 2.0: Refining XL-MS data acquisition through enhanced quality control | en_US |
| Type | Article | en_US |
| DOI | https://doi.org/10.1021/acs.jproteome.3c00791 | |
| 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 | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | en_US |
| Affilliation | Department of Chemical Biology, Leibniz. Forschungsinstitut für Molekulare Pharmakologie (FMP). Berlin, Germany. | en_US |
| Affilliation | Department of Chemical Biology, Leibniz. Forschungsinstitut für Molekulare Pharmakologie (FMP). Berlin, Germany. | en_US |
| Affilliation | Universidade Estadual de Campinas. Dalton Mass Spectrometry Laboratory. Campinas, Brasil | en_US |
| Affilliation | Department of Chemical Biology, Leibniz. Forschungsinstitut für Molekulare Pharmakologie (FMP). Berlin, Germany. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | en_US |
| Subject | Cross-Linking | en_US |
| Subject | Mass Spectrometry | en_US |
| Subject | Quality Control | en_US |
| Subject | Computational Biology | en_US |
| Subject in Spanish | Espectrometría de Masas | en_US |
| Subject in Spanish | Control de Calidad | en_US |
| Subject in Spanish | Biología Computacional | en_US |
| Subject in French | Spectrométrie de masse | en_US |
| Subject in French | Contrôle de qualité | en_US |
| Subject in French | Biologie informatique | en_US |
| DeCS | Espectrometria de Massas | en_US |
| DeCS | Controle de Qualidade | en_US |
| DeCS | Biologia Computacional | en_US |
