M. Hoopmann

发表

Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data.

M. MacCoss, J. Canterbury, Christine C. Wu, 2008, Analytical chemistry.

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

J. Eng, M. Hoopmann, Tahmina A. Jahan, 2013, Proteomics.

Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry.

Gennifer E. Merrihew, M. MacCoss, Gennifer E Merrihew, 2010, Analytical chemistry.

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

R. Moritz, M. Hoopmann, 2013, Current opinion in biotechnology.

Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures.

Gennifer E. Merrihew, M. MacCoss, Gennifer E Merrihew, 2009, Journal of Proteome Research.

Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification.

Chad R. Weisbrod, J. Eng, M. Hoopmann, 2012, Journal of proteome research.

High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry.

M. MacCoss, Greg L. Finney, M. Hoopmann, 2007, Analytical chemistry.

Quantitative Proteomic and Interaction Network Analysis of Cisplatin Resistance in HeLa Cells

Chad R. Weisbrod, M. Hoopmann, J. Bruce, 2011, PloS one.

A Deeper Look into Comet—Implementation and Features

Michael J MacCoss, William Stafford Noble, William S Noble, 2015, Journal of The American Society for Mass Spectrometry.

Cross-linking Measurements of In Vivo Protein Complex Topologies*

Michael R Hoopmann, Chunxiang Zheng, Chad R Weisbrod, 2011, Molecular & Cellular Proteomics.

Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times.

Lukas Käll, Luminita Moruz, Magnus Rosenlund, 2013, Journal of proteome research.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study

Karl Mechtler, Michael J MacCoss, Jürgen Cox, 2019, Analytical chemistry.

SILACtor: software to enable dynamic SILAC studies.

M. Hoopmann, J. Bruce, J. Chavez, 2011, Analytical chemistry.

RESEARCH ARTICLE Open Access Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling

M. MacCoss, M. Nachman, W. Swanson, 2022 .

Identification of peptide features in precursor spectra using Hardklör and Krönik.

M. MacCoss, R. Moritz, M. Hoopmann, 2012, Current protocols in bioinformatics.

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

P. May, C. Laczny, L. Lebrun, 2020, Nature microbiology.

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.

Karl Mechtler, Andrew R Jones, Christoph H Borchers, 2020, Structure.

Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests*

Kristian E. Swearingen, R. Moritz, J. Aitchison, 2011, Molecular & Cellular Proteomics.

Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

Andrew R. Jones, J. Cox, A. Sali, 2020, 2007.00383.

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

Rohan B. H. Williams, A. Heintz‐Buschart, P. May, 2020, Nature Communications.

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

David D. Shteynberg, R. Moritz, E. Deutsch, 2015, Journal of The American Society for Mass Spectrometry.

Robust determination of differential abundance in shotgun proteomics using nonparametric statistics.

D. Geman, R. Moritz, M. Hoopmann, 2018, Molecular omics.

Systems-level patterns in biological processes are changed under prolongevity interventions and across biological age

A. Magis, Gustavo Glusman, C. Lausted, 2022, medRxiv.

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

Chris Sander, Eric W. Deutsch, Emek Demir, 2016, Cell.

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

William Stafford Noble, Yang Young Lu, Charles E. Grant, 2022, bioRxiv.

Structural surfaceomics reveals an AML-specific conformation of Integrin-β2 as a CAR-T therapy target

R. Moritz, Lan Huang, Fernando Salangsang, 2022, bioRxiv.

A druggable oxidative folding pathway in the endoplasmic reticulum of human malaria parasites

R. Moritz, M. Hoopmann, V. Muralidharan, 2020, bioRxiv.

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks

Paul Wilmes, Thomas Sauter, Patrick May, 2015, npj Biofilms and Microbiomes.

2021 Special Issue on Software Tools and Resources: Finding the Right Tools for the Job.

M. Hoopmann, S. Weintraub, Magnus Palmblad, 2021, Journal of proteome research.

Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.

David D. Shteynberg, M. MacCoss, R. Moritz, 2023, Journal of proteome research.

The 5300-year-old Helicobacter pylori genome of the Iceman

Thomas Rattei, Rudolf Grimm, Robert L Moritz, 2016, Science.

Decreased Gap Width in a Cylindrical High-Field Asymmetric Waveform Ion Mobility Spectrometry Device Improves Protein Discovery.

Kristian E. Swearingen, U. Kusebauch, R. Moritz, 2015, Analytical chemistry.

Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics.

Michael J MacCoss, Michael R Hoopmann, Xianhua Yi, 2008, Analytical chemistry.

Quantitative proteogenomic profiling of epidermal barrier formation in vitro.

R. Moritz, J. Watts, M. Hoopmann, 2015, Journal of dermatological science.

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

O. Fiehn, P. Malfertheiner, U. Kusebauch, 2018, Current Biology.

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

P. Manghi, N. Segata, U. Kusebauch, 2021, Current Biology.

Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector

Kristian E. Swearingen, U. Kusebauch, R. Moritz, 2021, bioRxiv.

DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics

Robert L Moritz, Mukul K Midha, David S Campbell, 2020, Nature Communications.

Lung proteomic biomarkers associated with chronic obstructive pulmonary disease

E. Silverman, R. Moritz, R. Bueno, 2021, medRxiv.

Absence of full-length dystrophin impairs normal maturation and contraction of cardiomyocytes derived from human induced pluripotent stem cells.

R. Moritz, M. Regnier, Deok‐Ho Kim, 2019, Cardiovascular research.

Discovery and Visualization of Uncharacterized Drug–Protein Adducts Using Mass Spectrometry

M. MacCoss, R. Moritz, T. Davis, 2021, bioRxiv.

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

Nitin S. Baliga, Paul Wilmes, Patrick May, 2014, Nature Communications.

Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

Yi Shi, Karl Mechtler, Lan Huang, 2018 .

Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking.

Michael J MacCoss, David Baker, Alex Zelter, 2010, Journal of proteome research.

Kinetochore Biorientation in Saccharomyces cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex

J. Yates, M. MacCoss, R. Moritz, 2014, Genetics.

The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling

Massimiliano Bonomi, Michael J MacCoss, Daniel Jaschob, 2015, Nature Communications.

Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.

David D. Shteynberg, R. Moritz, J. Eng, 2023, Journal of proteome research.

Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector

Kristian E. Swearingen, U. Kusebauch, R. Moritz, 2021, mBio.

SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry.

R. Moritz, M. Hoopmann, Luis Mendoza, 2021, Journal of proteome research.

A redox-active crosslinker reveals an essential and inhibitable oxidative folding network in the endoplasmic reticulum of malaria parasites

R. Moritz, M. Hoopmann, V. Muralidharan, 2021, PLoS pathogens.

Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project.

Magnus Palmblad, Nuno Bandeira, Bin Xia, 2020, Journal of proteome research.

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

Eric W. Deutsch, Luis Mendoza, Mukul Kumar Midha, 2019, bioRxiv.

ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.

Samuel H Payne, Yasset Perez-Riverol, Magnus Palmblad, 2018, Journal of biomolecular techniques : JBT.

StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline.

Luis Mendoza, Robert L Moritz, Michael R Hoopmann, 2018, Journal of proteome research.

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.

Brendan MacLean, Magnus Palmblad, Olga Vitek, 2017, Journal of proteome research.

Kojak: efficient analysis of chemically cross-linked protein complexes.

Michael J MacCoss, Alex Zelter, Trisha N Davis, 2015, Journal of proteome research.

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

William Stafford Noble, Barbara Frewen, Michael J. MacCoss, 2014, Journal of proteome research.

iPRG-2015 Proteome Informatics Research Group Study : Differential Abundance Analysis in Label-free Quantitative Proteomics

J. Cottrell, M. Hoopmann, E. Kapp, 2014 .

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

P. May, C. Laczny, L. Lebrun, 2020, Nature Microbiology.

Testing and Validation of Computational Methods for Mass Spectrometry.

Henning Hermjakob, Oliver Kohlbacher, Laurent Gatto, 2016, Journal of proteome research.

The state of the human proteome in 2012 as viewed through PeptideAtlas.

Eric W Deutsch, Robert L Moritz, Michael R Hoopmann, 2013, Journal of proteome research.

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

Chad R. Weisbrod, M. Senko, M. Hoopmann, 2013, Journal of proteomics.

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

David D. Shteynberg, Henry H. N. Lam, L. Hood, 2016 .

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

Luis Mendoza, Eric W Deutsch, Robert L Moritz, 2016, Journal of The American Society for Mass Spectrometry.

Comparison of database search strategies for high precursor mass accuracy MS/MS data.

Michael J MacCoss, Brendan MacLean, Michael R Hoopmann, 2010, Journal of proteome research.

The fasted/fed mouse metabolic acetylome: N6-acetylation differences suggest acetylation coordinates organ-specific fuel switching.

J. Eng, M. Hoopmann, J. Bruce, 2011, Journal of proteome research.

Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers

Lance T. Pflieger, J. Roach, N. Schork, 2023, Communications biology.

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

M. MacCoss, M. Nachman, W. Swanson, 2011, BMC genomics.

Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences.

Lukas Käll, Luminita Moruz, Oliver Serang, 2012, Journal of proteome research.

A protein standard that emulates homology for the characterization of protein inference algorithms

Samuel H Payne, Yasset Perez-Riverol, Magnus Palmblad, 2017, bioRxiv.

Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data.

M. MacCoss, J. Canterbury, Christine C. Wu, 2008, Analytical chemistry.

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

Henning Hermjakob, Eric W. Deutsch, John Boyle, 2012, BMC Bioinformatics.

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

Matthew D Dean, M. MacCoss, M. Nachman, 2011, BMC Genomics.

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks

C. Laczny, L. Lebrun, P. Wilmes, 2015, npj Biofilms and Microbiomes.