MSPypeline: a python package for streamlined data analysis of mass spectrometry-based proteomics

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Abstract:

        Abstract
        
          Summary
          Mass spectrometry-based proteomics is increasingly employed in biology and medicine. To generate reliable information from large datasets and ensure comparability of results, it is crucial to implement and standardize the quality control of the raw data, the data processing steps and the statistical analyses. MSPypeline provides a platform for importing MaxQuant output tables, generating quality control reports, data preprocessing including normalization and performing exploratory analyses by statistical inference plots. These standardized steps assess data quality, provide customizable figures and enable the identification of differentially expressed proteins to reach biologically relevant conclusions.
        
        
          Availability and implementation
          The source code is available under the MIT license at https://github.com/siheming/mspypeline with documentation at https://mspypeline.readthedocs.io. Benchmark mass spectrometry data are available on ProteomeXchange (PXD025792).
        
        
          Supplementary information
          Supplementary data are available at Bioinformatics Advances online.

SEEK ID: https://seek.lisym.org/publications/371

DOI: 10.1093/bioadv/vbac004

Projects: C-TIP-HCC network, Forschungsnetzwerk LiSyM-Krebs, LiSyM network, SMART-NAFLD

Publication type: Journal

Journal: Bioinformatics Advances

Editors: Alex Bateman

Citation: Bioinformatics Advances 2(1),vbac004

Date Published: 2022

Registered Mode: by DOI

Authors: Simon Heming, Pauline Hansen, Artyom Vlasov, Florian Schwörer, Stephen Schaumann, Paulina Frolovaitė, Wolf-Dieter Lehmann, Jens Timmer, Marcel Schilling, Barbara Helm, Ursula Klingmüller

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Submitter

Ina Biermayer

Citation

Heming, S., Hansen, P., Vlasov, A., Schwörer, F., Schaumann, S., Frolovaitė, P., Lehmann, W.-D., Timmer, J., Schilling, M., Helm, B., & Klingmüller, U. (2022). MSPypeline: a python package for streamlined data analysis of mass spectrometry-based proteomics. In A. Bateman (Ed.), Bioinformatics Advances (Vol. 2, Issue 1). Oxford University Press (OUP). https://doi.org/10.1093/bioadv/vbac004

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Created: 2nd Aug 2023 at 11:39

Last updated: 8th Mar 2024 at 07:44

MSPypeline: a python package for streamlined data analysis of mass spectrometry-based proteomics

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