Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data.

Literature DB >> 32902283

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data.

Laurent Gatto¹, Sebastian Gibb², Johannes Rainer³.

Abstract

We present version 2 of the MSnbase R/Bioconductor package. MSnbase provides infrastructure for the manipulation, processing, and visualization of mass spectrometry data. We focus on the new on-disk infrastructure, that allows the handling of large raw mass spectrometry experiments on commodity hardware and illustrate how the package is used for elegant data processing, method development, and visualization.

Keywords: Bioconductor; R; mass spectrometry; metabolomics; proteomics; reproducible research; software; visualization

Mesh：

Year: 2020 PMID： 32902283 DOI： 10.1021/acs.jproteome.0c00313

Source DB: PubMed Journal: J Proteome Res ISSN： 1535-3893 Impact factor: 4.466

Keyword Cloud
Cited

15 in total

Review 1. Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data.

Authors: Zhiqiang Pang; Guangyan Zhou; Jessica Ewald; Le Chang; Orcun Hacariz; Niladri Basu; Jianguo Xia
Journal: Nat Protoc Date: 2022-06-17 Impact factor: 17.021

2. Deciphering the immunopeptidome in vivo reveals new tumour antigens.

Authors: Alex M Jaeger; Lauren E Stopfer; Ryuhjin Ahn; Emma A Sanders; Demi A Sandel; William A Freed-Pastor; William M Rideout; Santiago Naranjo; Tim Fessenden; Kim B Nguyen; Peter S Winter; Ryan E Kohn; Peter M K Westcott; Jason M Schenkel; Sean-Luc Shanahan; Alex K Shalek; Stefani Spranger; Forest M White; Tyler Jacks
Journal: Nature Date: 2022-06-15 Impact factor: 69.504

3. Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier Transform Mass Spectrometry Experiments.

Authors: Robert M Flight; Joshua M Mitchell; Hunter N B Moseley
Journal: Metabolites Date: 2022-06-02

4. Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments.

Authors: Tom S Smith; Anna Andrejeva; Josie Christopher; Oliver M Crook; Mohamed Elzek; Kathryn S Lilley
Journal: ACS Meas Sci Au Date: 2022-03-09

5. MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses.

Authors: Austin V Carr; Brian L Frey; Mark Scalf; Anthony J Cesnik; Zach Rolfs; Kyndal A Pike; Bing Yang; Mark P Keller; David F Jarrard; Michael R Shortreed; Lloyd M Smith
Journal: J Proteome Res Date: 2022-01-24 Impact factor: 5.370

6. ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis.

Authors: Alyssa Imbert; Magali Rompais; Mohammed Selloum; Florence Castelli; Emmanuelle Mouton-Barbosa; Marion Brandolini-Bunlon; Emeline Chu-Van; Charlotte Joly; Aurélie Hirschler; Pierrick Roger; Thomas Burger; Sophie Leblanc; Tania Sorg; Sadia Ouzia; Yves Vandenbrouck; Claudine Médigue; Christophe Junot; Myriam Ferro; Estelle Pujos-Guillot; Anne Gonzalez de Peredo; François Fenaille; Christine Carapito; Yann Herault; Etienne A Thévenot
Journal: Sci Data Date: 2021-12-03 Impact factor: 6.444

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data.

Review 1. Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data.

2. Deciphering the immunopeptidome in vivo reveals new tumour antigens.

3. Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier Transform Mass Spectrometry Experiments.

4. Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments.

5. MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses.

6. ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis.

7. In silico deconjugation of glucuronide conjugates enhances tandem mass spectra library annotation of human samples.

8. A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides.

9. Multiple Imputation Approaches Applied to the Missing Value Problem in Bottom-Up Proteomics.

10. MSLibrarian: Optimized Predicted Spectral Libraries for Data-Independent Acquisition Proteomics.