Abstract
For large-scale and standardized applications in mass spectrometry- (MS-) based proteomics automation of each step is essential. Here we present high-throughput sample preparation solutions for balancing the speed of current MS-acquisitions and the time needed for analytical workup of body fluids. The discussed workflows reduce body fluid sample complexity and apply for both bottom-up proteomics experiments and top-down protein characterization approaches. Various sample preparation methods that involve solid-phase extraction (SPE) including affinity enrichment strategies have been automated. Obtained peptide and protein fractions can be mass analyzed by direct infusion into an electrospray ionization (ESI) source or by means of matrix-assisted laser desorption ionization (MALDI) without further need of time-consuming liquid chromatography (LC) separations.
Highlights
Sample preparation of biological specimens is an essential part in any mass spectrometry- (MS-) based proteomics experiment since body fluids as well as tissue sections are highly complex in terms of variety in components and their concentrations
We have developed fully automated sample preparation pipelines that allow MS-profiling of body fluids at HTP (500– 1000 samples per 24 hours) and have been applied in clinical studies based on biobanked samples [2,3,4]
High-throughput analysis is required in particular for clinical samples when MS-based proteomics is applied to case/control disease studies
Summary
Sample preparation of biological specimens is an essential part in any mass spectrometry- (MS-) based proteomics experiment since body fluids as well as tissue sections are highly complex in terms of variety in components and their concentrations. We have developed fully automated sample preparation pipelines that allow MS-profiling of body fluids at HTP (500– 1000 samples per 24 hours) and have been applied in clinical studies based on biobanked samples [2,3,4]. Most of these so-called peptide and protein profiles were acquired on matrix-assisted laser desorption ionization (MALDI). Cerebrospinal fluid (CSF) is a relatively “clean” sample and can often be further used without extensive preparation steps It can not be obtained and if so only in small volumes. All workflows discussed in the current review are based on solidphase extraction (SPE) and can be combined with HTP bottom-up as well as top-down proteomics approaches
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