Wisconsin Alumni Research Foundation

Michael S Westphall

Joshua J Coon

Lloyd M Smith

Robert H Blick

Mark Andrew Scalf

Derek James Bailey

Brian L Frey

Hua Qin

William Travis Berggren

Daniel D Ebeling

Nicholas William Kwiecien

Timothy James Donohue

Graeme C McAlister

Amelia Corinne Peterson

Derek J Bailey

Xiaoyu Chen

Rachelle A S Lemke

H Blick Robert

The present invention provides a platform that enables codeless generation of online mass spectrometry data exploration portals. The platform facilitates upload of generic spreadsheets containing processed mass spectrometry results (e.g., peak tables) and enables on-the-fly hierarchical organization of data. Following data upload, platform users can select individual visualizations to add to their custom web portal from a menu of options. Based on these selections, a complete webpage is constructed with all associated functionality embedded. These custom web portals can then be shared with collaborators and other researchers at the discretion of the creator via a developed user permissions sharing scheme.

Web-based data upload and visualization platform enabling creation of code-free exploration of MS-based omics data

The present invention provides methods for controllably forming a layer of amorphous ice and other amorphous solids on a substrate, and also provides cryo-electron microscopy (cryo-EM) sample preparation methods and systems that utilize in vacuo formation of amorphous ice and other solids. Formation of the amorphous solid layer can be independent of the deposition of sample molecules to be analyzed using electron microscopy, and allows for the generation of a uniformly thick layer. Optionally, mass spectrometry instruments are used to generate and purify molecules deposited on the generated amorphous solid layer. The techniques and systems described herein can deliver near ideal cryo-EM sample preparation to greatly increase resolution, sensitivity, scope, and throughput of cryo-EM protein imaging, and therefore greatly impact the field of structural biology.

Gas phase sample preparation for cryo-electron microscopy

Imaging by cryo-electron microscopy (cryo-EM) requires that a sample be encased in an amorphous solid, such as amorphous ice. In current cryo-EM preparation systems, once the sample has been deposited on an EM grid and coated in the amorphous solid, the EM grid must be removed from vacuum and then transferred into the vacuum of the cryo-EM system. As a result, samples deposited on the grid are exposed to damage and contamination. The present invention provides improved EM grid handling systems and devices compatible with advanced cryo-EM sample preparation techniques and which reduce or eliminate exposure of the sample on the grid to atmosphere and elevated temperatures. These methods and devices will also significantly reduce handling time and complexities associated with cryo-EM sample preparation.

Retractable ion guide, grid holder, and technology for removal of cryogenic sample from vacuum

The present invention provides methods for controllably forming a layer of amorphous ice and other amorphous solids on a substrate, and also provides cryoelectron microscopy (cryo-EM) sample preparation methods and systems that utilize in vacuo formation of amorphous ice and other solids. Formation of the amorphous solid layer can be independent of the deposition of sample molecules to be analyzed using electron microscopy, and allows for the generation of a uniformly thick layer. Optionally, mass spectrometry instruments are used to generate and purify molecules deposited on the generated amorphous solid layer. The techniques and systems described herein can deliver near ideal cryo-EM sample preparation to greatly increase resolution, sensitivity, scope, and throughput of cryo-EM protein imaging, and therefore greatly impact the field of structural biology.

Described herein are mass spectrometry systems and methods which improve the accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference and co-isolation of impurities through gas-phase purification. During the gas-phase purification, the mass-to-charge ratios of precursor ions within at least a selected range are selectively changed allowing ions having similar unmodified mass-to-charge ratios to be separated before further isolation, fragmentation or analysis.

Gas-phase purification for accurate isobaric tag-based quantification

Enzymes for producing non-straight-chain fatty acids, microorganisms comprising the enzymes, and in vivo and in vitro uses of the enzymes. Provided are enzymes capable of producing various non-straight-chain fatty acids, including branched-chain fatty acids, cyclic fatty acids, and furan-containing fatty acids. The enzymes include RSP2144, RSP1091, and RSP1090 fromand homologs thereof. The enzymes can be purified to produce non-straight-chain fatty acids in vitro or expressed in microorganisms to produce non-straight-chain fatty acids in vivo. The microorganisms can be fine-tuned to produce a specific type of non-straight-chain fatty acid by expressing, overexpressing, or deleting the enzymes in various combinations.

Enzymes for producing non-straight-chain fatty acids

The invention provides methods, systems and algorithms for identifying high-resolution mass spectra. In some embodiments, an analyte is ionized and analyzed using high-resolution mass spectrometry (MS) at high mass accuracy (such as &#x2264;75 ppm or &#x2264;30 ppm) and the obtained mass spectra are matched with one or more prospective candidate molecules or chemical formulas. The invention provide, for example, methods and systems wherein the possible fragments that can be generated from the candidate molecules or chemical formulas are determined as well as the masses of each of these fragments. The invention provide, for example, methods and systems wherein the high-resolution mass spectra are then compared with the calculated fragment masses for each of the candidate molecules or chemical formula, and the portion of the high-resolution mass spectra that corresponds or can be explained by the calculated fragment masses is determined.

High mass accuracy filtering for improved spectral matching of high-resolution gas chromatography-mass spectrometry data against unit-resolution reference databases

A method of identifying a related peak set from MS1 spectra data is provided. An intensity peak is selected from MS1 spectra data generated for a sample by a tandem mass spectrometer. A peak location is identified for the selected intensity peak. An intensity score is calculated from the MS1 spectra data for each of a plurality of possible related peak locations based on an intensity value associated with each of the plurality of possible related peak locations. Whether or not any of the plurality of possible related peak locations forms a related peak set is determined based on the calculated intensity score for each of the plurality of possible related peak locations.

Identification of related peptides for mass spectrometry processing

Described herein are mass spectrometry systems and methods which utilize a dynamic a new data acquisition/instrument control methodology. These systems and methods employ novel artificial intelligence algorithms to greatly increase quantitative and/or identification accuracy during data acquisition. In an embodiment, the algorithms can adapt the instrument methods and systems during data acquisition to direct data acquisition resources to increase quantitative or identification accuracy of target analytes, such as proteins, peptides, and peptide fragments.

Precursor selection using an artificial intelligence algorithm increases proteomic sample coverage and reproducibility

An active detector and methods for detecting molecules, including large molecules such as proteins and oligonucleotides, at or near room temperature based on the generation of electrons via field emission (FE) and/or secondary electron emission (SEE). The detector comprises a semiconductor membrane having an external surface that is contacted by one or more molecules, and an internal surface having a thin metallic layer or other type of electron emitting layer. The kinetic energy of molecules contacting the semiconductor membrane is transferred through the membrane and induces the emission of electrons from the emitting layer. An electron detector, which optionally includes means for electron amplification, is positioned to detect the emitted electrons.

Molecule mass detection via field emission of electrons from membranes

A fast and sensitive method and device for protein sequencing are disclosed. The method uses a combination of Edman degradation chemistry and mass spectrometry to sequence proteins and polypeptides. A peptide degradation reaction is performed on a polypeptide or protein ion reactant in the gas phase. The reaction yields a first ion product corresponding to a first amino acid residue of the polypeptide or protein reactant and a polypeptide or protein fragment ion. The mass-to-charge ratio for the first ion product, or the polypeptide or protein fragment ion, or both, is then determined. The first amino acid residue of the polypeptide or protein reactant is then identified from the mass-to-charge ratio so determined.

Protein/peptide sequencing by chemical degradation in the gas phase

The present invention provides systems, devices, device components and structures for modulating the intensity and/or energies of electrons, including a beam of incident electrons. In some embodiments, for example, the present invention provides nano-structured semiconductor membrane structures capable of generating secondary electron emission. Nano-structured semiconductor membranes of this aspect of the present invention include membranes having an array of nanopillar structures capable of providing electron emission for amplification, filtering and/or detection of incident radiation, for example secondary electron emission and/or field emission. Nano-structured semiconductor membranes of the present invention are useful as converters wherein interaction of incident primary electrons and nanopillars of the nanopillar array generates secondary emission. Nano-structured semiconductor membranes of this aspect of the present invention are also useful as directed charge amplifiers wherein secondary emission from a nanopillar array provides gain functionality for increasing the intensity of radiation comprising incident electrons.

Nanopillar arrays for electron emission

This invention provides methods, devices and device components for preparing ions from liquid samples containing chemical species and methods and devices for analyzing chemical species in liquid samples. The present invention provides an ion source for generating analyte ions having a selected charge state distribution, such as a reduced charged state distribution, that may be effectively interfaced with a variety of charged particle analyzers, including virtually any type of mass spectrometer.

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Madison, WI, United States of America

Michael S Westphall