A state-of-the-art machine learning pipeline for the analysis of spatial proteomics data

Laurent Gatto1, 2, Lisa M. Breckels1, 2, Thomas Naake1, 2, Samuel Wieczorek3, Thomas Burger3 and Kathryn S. Lilley2

1 Introduction and objectives

Organelle proteomics, or spatial proteomics, is the systematic study of protein sub-cellular localisation. Here, we focus on high-throughput quantitative mass spectrometry-based techniques such as LOPIT and PCP and demonstrate a robust and sound analysis pipeline using state-of-the-art and novel machine learning algorithms implemented in the pRoloc4, 5 R/Bioconductor package.

2 Methods

We illustrate the pipeline using relevant real-world data sets available from the pRolocdata package4, documenting importing data available in spreadsheet formats into the R environment, missing data imputation, data quality control, facilitated organelle marker assignment, protein clustering, identification of new, non-labelled organelles using semi-supervised machine learning6, protein classification and data visualisation.

3 Results and Discussion

While the pipeline automates some fundamental requirements such as parameter optimisation via cross-validation, imputation of missing values, organelle markers definition and allows the user to assess such crucial parameters, we also highlight the importance of informed user decisions and validation. Despite the requirement for elaborate and cross-disciplinary tool sets, the biologists must remain in control of the fate of their data and in a position to make informed decisions about the data analysis and validity of the results to produce biologically relevant and meaningful interpretation.

4 Conclusions

Complex high dimensional data analysis is a challenging task. While statistics and computer science provide the wider research community with several algorithms and best practice, their application is often difficult and may at times, when underlying assumptions are not met, lead to misleading claims. We show how such state-of-the-art methods can be applied on well-defined and annotated data in a coherent, traceable and reproducible pipeline.

5 Resources



Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK


Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK


Universite Grenoble-Alpes, CEA (iRSTV/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France

Author: Laurent Gatto

Created: 2014-10-02 Thu 12:03

Emacs 24.3.1 (Org mode 8.2.7c)