Applications of multivariate analysis and unsupervised machine learning to ToF-SIMS images of organic, bioorganic, and biological systems

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging offers a powerful, label-free method for exploring organic, bioorganic, and biological systems. The technique is capable of very high spatial resolution, while also producing an enormous amount of information about the chemical and molecular composition of a surface. However, this information is inherently complex, making interpretation and analysis of the vast amount of data produced by a single ToF-SIMS experiment a considerable challenge. Much research over the past few decades has focused on the application and development of multivariate analysis (MVA) and machine learning (ML) techniques that find meaningful patterns and relationships in these datasets. Here, we review the unsupervised algorithms—that is, algorithms that do not require ground truth labels—that have been applied to ToF-SIMS images, as well as other algorithms and approaches that have been used in the broader family of mass spectrometry imaging (MSI) techniques. We first give a nontechnical overview of several commonly used classes of unsupervised algorithms, such as matrix factorization, clustering, and nonlinear dimensionality reduction. We then review the application of unsupervised algorithms to various organic, bioorganic, and biological systems including cells and tissues, organic films, residues and coatings, and spatially structured systems such as polymer microarrays. We then cover several novel algorithms employed for other MSI techniques that have received little attention from ToF-SIMS imaging researchers. We conclude with a brief outline of potential future directions for the application of MVA and ML algorithms to ToF-SIMS images.

Synergistic influence of collagen I and BMP 2 drives osteogenic differentiation of mesenchymal stem cells: A cell microarray analysis

Cell microarrays are a novel platform for the high throughput discovery of new biomaterials. By re-creating a multitude of cell microenvironments on a single slide, this approach can identify the optimal surface composition to drive a desired cell response. To systematically study the effects of molecular microenvironments on stem cell fate, we designed a cell microarray based on parallel exposure of mesenchymal stem cells (MSCs) to surface-immobilised collagen I (Coll I) and bone morphogenetic protein 2 (BMP 2). This was achieved by means of a reactive coating on a slide surface, enabling the covalent anchoring of Coll I and BMP 2 as microscale spots printed by a robotic contact printer. The surface between the printed protein spots was passivated using poly (ethylene glycol) bisamine 10,000Da (A-PEG). MSCs were then captured and cultured on array spots composed of binary mixtures of Coll I and BMP 2, followed by automated image acquisition and quantitative, multi-parameter analysis of cellular responses. Surface compositions that gave the highest osteogenic differentiation were determined using Runx2 expression and calcium deposition. Quantitative single cell analysis revealed subtle concentration-dependent effects of surface-immobilised proteins on the extent of osteogenic differentiation obscured using conventional analysis. In particular, the synergistic interaction of Coll I and BMP 2 in supporting osteogenic differentiation was confirmed. Our studies demonstrate the value of cell microarray platforms to decipher the combinatorial interactions at play in stem cell niche microenvironments.

Low temperature thermal dependent Filgrastim adsorption behavior detected with ToF-SIMS

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) detected changes in Filgrastim (granulocyte colony stimulating growth factor, G-CSF) adsorption behavior at a solid interface when exposed to temperatures as low as 35 °C, i.e., before thermal denaturation, was detected by circular dichroism (CD) or dynamic light scattering (DLS). Biopharmaceuticals rely on maintaining sufficient conformation to impart correct biological function in vivo. Stability of such molecules is critical during synthesis, storage, transport, and administration. CD analysis indicated loss of structure at temperatures greater than ~60 °C, while DLS detected aggregation at ~42 °C. Furthermore, we demonstrate the nature of G-CSF interaction with a surface was altered rapidly and at relatively low temperatures. Specifically, after 10 min thermal treatment, changes in adsorption behavior occurred at 35 °C indicated by principal component analysis of spectra as primarily due to increasing yields of methionine fragments. This was likely to be due to either altering the preferential protein orientation upon adsorption or greater denaturation exposing the hydrophobic core. This investigation demonstrates the sensitivity of ToF-SIMS in studying biopharmaceutical adsorption and conformational change and can assist with studies into promoting their stability.