Matrices and systems for preservation of biomolecules in vacuum

A method for preparing a sample comprising the steps of:

• a) contacting a substrate surface with a liquid or semiliquid substance thereby forming a matrix layer of the liquid or semiliquid substance on the substrate surface;
• and
• b) depositing target molecules having an initial structure onto or within the matrix layer under vacuum;
• wherein the target molecules are at least partially embedded in the matrix layer and wherein the initial structure of at least a portion of the target molecules is maintained while within the vacuum.

A method for preparing a sample for electron microscopy (EM) comprising the steps of:

• a) contacting a substrate surface with a liquid or semiliquid substance thereby forming a matrix layer of the liquid or semiliquid substance on the substrate surface, wherein the substrate is an electron microscopy (EM) grid;
• b) generating a first distribution of precursor ions from a sample of target molecules;
• c) separating a portion of ions from the first distribution of precursor ions according to mass-to-charge ratios of the precursor ions, thereby generating separated ions;
• d) generating an ion beam containing the separated ions, and
• e) directing the ion beam to the substrate surface under vacuum;
• thereby depositing target molecule ions onto or within the matrix layer, wherein the target molecule ions are partially embedded in the matrix layer and wherein the structure of at least a portion of the target molecule ions is retained.

A system for depositing target molecules on a substrate comprising:

• a) an ion source able to generate ions from a sample of molecules;
• b) first ion focusing optics in fluid communication with the ion source;
• c) ion separation optics in fluid communication with the first ion focusing optics, wherein the first ion focusing optics are able to transport ions from the ion source to the ion separation optics, and wherein the ion separation optics are able to separate ions according to the mass-to-charge ratios of the ions;
• d) a sample chamber in fluid communication with the ion separation optics, wherein the sample chamber maintains a vacuum and contains a substrate able to be inserted into and removed from the sample chamber while maintaining the vacuum;
• and
• e) a controller, operably connected to the first ion focusing optics, the ion separation optics, and the sample chamber, where the controller controls the first ion focusing optics and ion separation optics so as to:
• i) transport the ions from the ion source to the ion separation optics;
• ii) generate a first distribution of precursor ions from the transported ions;
• iii) isolate a target range of mass-to-charge ratios within the first distribution of precursor ions, thereby generating separated ions;
• iv) generate an ion beam comprising the separated ions;
• and
• v) contacting the substrate in the sample chamber with the ion beam, thereby depositing separated ions on the substrate under a vacuum.