Search results for: Michael R. Hoopmann

Items from 1 to 20 out of 20 results

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The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals

Frank Maixner, Dmitrij Turaev, Amaury Cazenave-Gassiot, Marek Janko, more

Current Biology > 2018 > 28 > 14 > 2348-2355.e9

The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary...

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An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results

Michael R. Hoopmann, Luis Mendoza, Eric W. Deutsch, David Shteynberg, more

Journal of The American Society for Mass Spectrometry > 2016 > 27 > 11 > 1728-1734

Protein–protein interactions are an important element in the understanding of protein function, and chemical cross-linking shotgun mass spectrometry is rapidly becoming a routine approach to identify these specific interfaces and topographical interactions. Protein cross-link data analysis is aided by dozens of algorithm choices, but hindered by a lack of a common format for representing results....

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Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Ulrike Kusebauch, David S. Campbell, Eric W. Deutsch, Caroline S. Chu, more

Cell > 2016 > 166 > 3 > 766-778

The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here, we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins...

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reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

David Shteynberg, Luis Mendoza, Michael R. Hoopmann, Zhi Sun, more

Journal of The American Society for Mass Spectrometry > 2015 > 26 > 11 > 1837-1847

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called...

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Quantitative proteogenomic profiling of epidermal barrier formation in vitro

Jason M. Winget, Julian D. Watts, Michael R. Hoopmann, Teresa DiColandrea, more

Journal of Dermatological Science > 2015 > 78 > 3 > 173-180

The barrier function of the epidermis is integral to personal well-being, and defects in the skin barrier are associated with several widespread diseases. Currently there is a limited understanding of system-level proteomic changes during epidermal stratification and barrier establishment.Here we report the quantitative proteogenomic profile of an in vitro reconstituted epidermis at three time points...

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A Deeper Look into Comet—Implementation and Features

Jimmy K. Eng, Michael R. Hoopmann, Tahmina A. Jahan, Jarrett D. Egertson, more

Journal of The American Society for Mass Spectrometry > 2015 > 26 > 11 > 1865-1874

The Comet database search software was initially released as an open source project in late 2012. Prior to that, Comet existed as the University of Washington’s academic version of the SEQUEST database search tool. Despite its availability and widespread use over the years, some details about its implementation have not been previously disseminated or are not well understood. We address a few of these...

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Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research

Chad R. Weisbrod, Michael R. Hoopmann, Michael W. Senko, James E. Bruce

Journal of Proteomics > 2013 > 88 > Complete > 109-119

A novel dual cell linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) and its performance characteristics are reported. A linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer has been modified to incorporate a LTQ-Velos mass spectrometer. This modified instrument features efficient ion accumulation and fast MS/MS acquisition capabilities of...

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Current algorithmic solutions for peptide-based proteomics data generation and identification

Michael R Hoopmann, Robert L Moritz

Current Opinion in Biotechnology > 2013 > 24 > 1 > 31-38

Peptide-based proteomic data sets are ever increasing in size and complexity. These data sets provide computational challenges when attempting to quickly analyze spectra and obtain correct protein identifications. Database search and de novo algorithms must consider high-resolution MS/MS spectra and alternative fragmentation methods. Protein inference is a tricky problem when analyzing large data...

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Comet: An open‐source MS/MS sequence database search tool

Jimmy K. Eng, Tahmina A. Jahan, Michael R. Hoopmann

PROTEOMICS > 13 > 1 > 22 - 24

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open‐source database search tools. Comet is open source, freely available, and based on one of the original sequence...

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SILACtor: Software To Enable Dynamic SILAC Studies

Michael R. Hoopmann, Juan D. Chavez, James E. Bruce

Analytical Chemistry > 2011 > 83 > 22 > 8403 - 8410

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The Fasted/Fed Mouse Metabolic Acetylome: N6-Acetylation Differences Suggest Acetylation Coordinates Organ-Specific Fuel Switching

Li Yang, Bhavapriya Vaitheesvaran, Kirsten Hartil, Alan J. Robinson, more

Journal of Proteome Research > 2011 > 10 > 9 > 4134 - 4149

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Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling

Matthew D Dean, Geoffrey D Findlay, Michael R Hoopmann, Christine C Wu, more

BMC Genomics > 2011 > 12 > 1 > 1-13

Background Seminal fluid plays an important role in successful fertilization, but knowledge of the full suite of proteins transferred from males to females during copulation is incomplete. The list of ejaculated proteins remains particularly scant in one of the best-studied mammalian systems, the house mouse (Mus domesticus), where artificial ejaculation techniques have proven inadequate. Here we...