Wisconsin Alumni Research Foundation

Promega Corporation

University of Virginia Patent Foundation

University of Florida Research Foundation, Incorporated

University of Illinois

Thermo Finnigan LLC

Coon, Joshua J.

Joshua J Coon

Michael S Westphall

Lloyd M Smith

Graeme C McAlister

Marjeta Urh

Michael Robert Shortreed

Michael M Rosenblatt

Donald F Hunt

John Edward Philip Syka

Brian L Frey

Derek James Bailey

Casey J Krusemark

Madhusudan Patel

Peter Jeremy Belshaw

Mark Andrew Scalf

Ryan Tyler Hilger

Neil L Kelleher

Daniel T Ladror

Nicholas William Kwiecien

Alex Hebert

Margaret F Phillips

Shane M Lamos

Douglas H Phanstiel

Jason Dale Russell

John Edward Syka

Jae C Schwartz

Shannon S Stahl

John E P Syka

Timothy James Donohue

Jarrod A Marto

Amelia Corinne Peterson

Derek J Bailey

Alireza Rahimi

Shane Lauson Hubler

Andreas F R Huhmer

Willard W Harrison

Arne Ulbrich

Harald Marx

Jarod A Marto

April L Jue

Rachelle A S Lemke

Craig D Wenger

Gheorghe Craciun

Andreas Fr Huhmer

John Ep Syka

John EP Syka

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

In shotgun proteomics, generally only a fraction of peptides from a parent protein are actually detected. Because a large portion of the protein sequence is not detected, it is often impossible to determine whether the expressed protein is present in a modified, spliced, or truncated form. Provided herein are methods and systems for analyzing polypeptides which allow for the increase of the mean sequence coverage of a protein concomitant with bioinformatics analysis in order to distinguish putative proteoforms with improved amino acid resolution. Aspects of the invention include (1) a deep sequencing strategy to provide more protein sequence coverage than is typically achieved, and (2) a computational approach to view protein expression across its full length and identify regions of the protein that are potentially subject to such regulation. This technology has global utility in proteomics and will be of particular use for the analysis of biosimilar protein drug therapeutics.

Method to map protein landscapes

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 reagents for instrumentation quality control and methods of use thereof. In particular, sets of peptides or other molecules are provided for evaluating the performance of instruments with mass spectrometry (MS) and/or liquid chromatography (LC) functionalities.

Quality control reagents and methods

The invention provides mass spectrometry methods, compositions and systems which enable a unique platform for analyte quantitation accessing very high degrees of multiplexing and accurate quantification, particularly well-suited for a range of quantitative analysis for proteomics applications. Embodiments of the present methods and systems combine isotopic coding agents characterized by very small differences in molecular mass with mass spectrometry methods providing large resolving power to provide relative or absolute analyte quantification in a large number of samples.

Neutron encoded mass tags for analyte quantification

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

Growing community of inventors

Middleton, WI, United States of America

Joshua J Coon