Sebastian Gibb

I am a medical doctor working as a consultant at the Department of Anaesthesiology and Intensive Care of the University Medicine Greifswald.

You could write me an e-mail or find me on: impactstory, researcherid, google scholar, orcid, dissemin, github, mastodon, stackoverflow.

Employment

• Dec 2014 - now: Department of Anaesthesiology and Intensive Care of the University Medicine Greifswald.

• Sep 2019 - Jun 2022: Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics of the University Hospital Leipzig.

• Jun 2014 - Nov 2014: Department of Anaesthesiology and Intensive Care of the University Hospital Carl Gustav Carus Dresden.

Education

• May 2022: Specialisation in Emergency Medicine (Zusatzweiterbildung Notfallmedizin).

• Jun 2021: Specialisation in Intensive Care Medicin (Zusatzweiterbildung spezielle Intensivmedizin).

• Dec 2019: European Diploma in Anaesthesiology and Intensive Care.

• Nov 2019: Certificate of Completion of Training (Facharzt) in Anaesthesia.

• Feb 2014 - May 2014: Visiting researcher in the Computational Proteomics Unit of the Cambridge Centre for Proteomics headed by Laurent Gatto.

• 2013: Staatsexamen in human medicine (physician exam), University of Leipzig.

Software

R packages

• MALDIquant: Quantitative Analysis of Mass Spectrometry Data. [github, cran, website]

• MALDIquantForeign: Import/Export routines for MALDIquant. [github, cran]

• readBrukerFlexData: Reads MS data in Bruker *flex format. [github, cran]

• readMzXmlData: Reads MS data in mzXML format. [github, cran]

• cleaver: In-silico cleavage of polypeptide sequences. [github, bioconductor]

• topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics. [github, bioconductor]

Contributions to R packages

• RforMassSpectrometry: R for Mass Spectrometry - R software for the analysis and interpretation of high throughput mass spectrometry assays. [github, website]

• synapter: Label-free data analysis pipeline for optimal identification and quantitation. [github, bioconductor]

• MSnbase: Base Functions and Classes for MS-based Proteomics. [github, bioconductor]

• mzID: A mzIdentML parser for R. [github, bioconductor]

• zoom: A spatial data visualization tool. [github, cran]

Publications

Publications

• Applying Machine Learning to Blood Count Data Predicts Sepsis with ICU Admission.
  D. Steinbach¹, P. Ahrens¹, M. Schmidt, M. Federbusch, L. Heuft, C. Lübbert, M. Nauck, M. Gründling, B. Isermann, S. Gibb², Th. Kaiser². 2024.
  Clinical Chemistry.
  DOI: 10.1093/clinchem/hvae001.

• A new machine-learning-based prediction of survival in patients with end-stage liver disease.
  S. Gibb, T. Berg, A. Herber, B. Isermann, and T. Kaiser. 2023.
  LaboratoriumsMedizin.
  DOI: 10.1515/labmed-2022-0162.

• Effective Amino Acid Sequencing of Intact Filgrastim by Multimodal Mass Spectrometry with Topdownr.
  M. Babović, P.V. Shliaha, S. Gibb, and O.N. Jensen. 2022.
  Journal of American Society for Mass Spectrometry.
  DOI: 10.1021/jasms.2c00193.

• A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R.
  J. Rainer, A. Vicini, L. Salzer, J. Stanstrup, J. M. Badia, S. Neumann, M. A. Stravs, V. V. Hernandes, L. Gatto, S. Gibb and M. Witting. 2022.
  Metabolites.
  DOI: 10.3390/metabo12020173.

• MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data.
  L. Gatto, S. Gibb and J. Rainer. 2020.
  Journal of Proteome Research 20: 1063-1069.
  DOI: 10.1021/acs.jproteome.0c00313. bioRxiv: 2020.04.29.067868.

• Notfall Sepsis: Erkennen, Diagnose, Therapie.
  M. Gründling, S. Gibb and A. Kühn. 2019.
  Intensivmed.up2date 15(03): 291-305.
  DOI: 10.1055/a-0793-7482. reprint.

• Maximizing Sequence Coverage in Top-Down Proteomics By Automated Multi-modal Gas-phase Protein Fragmentation.
  P.V. Shliaha¹, S. Gibb¹, V. Gorshkov, M.S. Jespersen, G.R. Andersen, D. Bailey, J. Schwartz, S. Eliuk, V. Schwämmle and O.N. Jensen. 2018.
  Analytical Chemistry 90: 12519-12526.
  DOI: 10.1021/acs.analchem.8b02344.

• The role of the ultra short-acting β₁-adrenoreceptor antagonist Landiolol in the treatment of atrial fibrillation: pharmacology, clinical application and current evidence in anaesthesiology, intensive care and emergency medicine (in German).
  S. Gibb and S. Rehberg. 2018.
  Anästhesiologie & Intensivmedizin 59: 407-421.
  reprint
  Disclosure of Potential Conflict of Interest: S. Gibb has nothing to disclose. S. Rehberg recieved personal fees for oral presentations from Amomed Pharma GmbH. He works as consultant for Amomed Pharma GmbH. He contributes to the planning and execution of LANDI-SEP.

• Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis.
  S. Gibb and K. Strimmer. 2015.
  Bioinformatics 31: 3156-3162.
  DOI: 10.1093/bioinformatics/btv334. arXiv: 1502.07959.

• Visualization of proteomics data using R and Bioconductor.
  L. Gatto, L.M. Breckels, T. Naake and S. Gibb. 2015.
  Proteomics 15: 1375-1389.
  DOI: 10.1002/pmic.201400392.

• Species determination of Culicoides biting midges via peptide profiling using matrix-assisted laser desorption ionization mass spectrometry.
  K.R. Uhlmann¹, S. Gibb¹, S. Kalkhof, U. Arroyo-Abad, C. Schulz, B. Hoffmann, F. Stubbins, S. Carpenter, M. Beer, M. von Bergen and R. Feltens. 2014.
  Parasites & Vectors 7: 392.
  DOI: 10.1186/1756-3305-7-392.

• MALDIquant: a versatile R package for the analysis of mass spectrometry data.
  S. Gibb and K. Strimmer. 2012.
  Bioinformatics 28: 2270-2271.
  DOI: 10.1093/bioinformatics/bts447. arXiv: 1203.5885.

(¹ equal contributors) (² equal senior contributors)

Book chapters

• Mass Spectrometry Analysis Using MALDIquant.
  S. Gibb and K. Strimmer. 2017.
  Springer International Publishing, Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry (Eds.: S. Datta and B. Mertens), pp. 101-124.
  DOI: 10.1007/978-3-319-45809-0_6. arXiv: 1607.03180.

• R for Proteomics.
  L. M. Breckels, S. Gibb, V. Petyuk and L. Gatto. 2016.
  The Royal Society of Chemistry, Proteome Informatics (Ed.: Conrad Bessant), pp. 321-364.
  DOI: 10.1039/9781782626732-00321.

Conference contributions

• Analysis of proteomic data using MALDIquant.
  S. Gibb and K. Strimmer. 2011.
  Proceedings of the 8th International Workshop on Computational Systems Biology, WCSB 2011 (June 6-8, 2011, Zurich, Switzerland), pp. 49-52.
  (reprint, poster).

M.D. thesis

• Development of a flexible bioinformatics platform for analyzing mass spectrometry data (in German).
  S. Gibb. 2015.
  URN: urn:nbn:de:bsz:15-qucosa-178678.
  (reprint).

Contact