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Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC-MS for biomarker discovery |
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| Authors: | Christin Christin Bischoff Rainer Horvatovich Péter |
| Institution: | a Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands b Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands |
| Abstract: | Label-free quantitative LC-MS profiling of complex body fluids has become an important analytical tool for biomarker and biological knowledge discovery in the past decade. Accurate processing, statistical analysis and validation of acquired data diversified by the different types of mass spectrometers, mass spectrometer parameter settings and applied sample preparation steps are essential to answer complex life science research questions and understand the molecular mechanism of disease onset and developments. This review provides insight into the main modules of label-free data processing pipelines with statistical analysis and validation and discusses recent developments. Special emphasis is devoted to quality control methods, performance assessment of complete workflows and algorithms of individual modules. Finally, the review discusses the current state and trends in high throughput data processing and analysis solutions for users with little bioinformatics knowledge. |
| Keywords: | 2D-LC-MS two dimensional liquid chromatography coupled to mass spectrometry AMT accurate mass and retention time tag APEX absolute protein expression APML annotated putative peptide markup language Cap-LC-MS LC-MS system equipped with capillary LC column (1 mm internal diameter) and using ionspray for ionization Chip LC LC-MS system equipped with nano-LC column (75 μm internal diameter) integrated in a microfluidic device and using electrospray for ionization CID collision induced dissociation DDA data dependent acquisition emPAI exponentially modified protein abundance ETD electron transfer dissociation FTMS Fourier transform ion cyclotron resonance mass spectrometry HDSS high dimensionality small sample size problem HUPO PSI Human Proteome Organization Proteomics Standard Initiative LC liquid chromatography LC-MS liquid chromatography coupled to mass spectrometry MEND matched filtration with experimental noise determination MRM multiple reaction monitoring MS mass spectrometry MS/MS fragment ion mass spectra of selected precursor ions MS-1 single stage mass spectrometry nano-LC liquid chromatography using chromatographic column of internal diameter smaller than 100 μm PTM post translational modification RSD relative standard deviation XML extensible markup language |
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