Proteome imaging: A closer look at life's organization

Abstract

Imaging the proteome is a term that is used in many different contexts. The term implies that the entire cohort of proteins and their modifications are visualized. This unfortunately is not the case. In this mini-review, a concise overview is provided on different imaging technologies that are currently used to investigate the structure, function and dynamics of proteins and their organization. These techniques have been selected for review based on the unique insights they provide in subsets of the proteome. These techniques have been illustrated with practical examples of their merits. Mass spectrometry-based imaging technologies are playing a key role in proteome research and have been reviewed in more detail. They hold the promise of detailed molecular insight in the spatial organization of living system.

Parallel processing of large datasets from NanoLC-FTICR-MS measurements

“…The contents of the first part of this algorithm depend on the type of mass spectrometer used, whereas the latter part of the algorithm is generic and thus applies to all kinds of different LC-MS datasets (e.g., obtained from quadrupole, ion trap, or time-of-flight instruments). Note that this approach also enables parallel processing of other two-dimensional mass spectral datasets, such as linescans in mass spectral images [5]. As an example, the PP-VLAM algorithm is described for datasets obtained from nanoLC-FTICR-MS experiments in Figure 1.…”

“…In this way the algorithm can be used for all types of LC-MS and LC-MS/MS datasets. The modular (workflow) nature of this approach also enables automated processing of other types of large mass spectral datasets such as the results obtained from high-resolution mass spectral imaging experiments [5].…”

“…However, it is evident that the amount and size of mass spectral datasets generated by modern mass spectrometers are incompatible with manual analysis. Examples of such large MS-based datasets are found in high-throughput proteomics experiments [4] as well as in high-resolution imaging MS experiments [5]. In a research lab real-time analysis of the experiments is pursued so that results can be used to adjust the parameters of the following experiment.…”

Visualization of Spatial Distribution of γ -Aminobutyric Acid in Eggplant (Solanum melongena) by Matrix-assisted Laser Desorption/Ionization Imaging Mass Spectrometry

“…IMS makes it possible to visualize the distribution of individual molecules in a tissue section without the use of antibodies, staining, or complicated pretreatment. 9,10 Direct analysis of a tissue section using IMS allows the detection of a wide range of endogenous molecules such as lipids, [10][11][12][13][14] glycolipids, [15][16][17] and peptides, 18,19 as well as the detection of administered pharmaceuticals. 20,21 IMS might be adapted to the comprehensive analyses of various metabolites in plants.…”

Cold electron and ion beams generated from trapped atoms

“…Focused ion beams ͑FIBs͒, 8 for example, provide nanoscale milling and imaging capabilities to the semiconductor industry, while secondary ion mass spectrometry ͑SIMS͒ ͑Ref. 9͒ is used to analyze the protein distribution in biological cells, 10 among others. Using electrons, so-called laser synchrotrons 11 generate ultrashort pulses of x-rays by nonlinear Thomson scattering, while ultrafast electron microscopes ͑UEMs͒ ͑Refs.…”