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Michael R. Hoopmann, Ph.D. - Publications

Institution:
University of Washington, Seattle, Seattle, WA
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49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Deutsch EW, Mendoza L, Shteynberg DD, Hoopmann MR, Sun Z, Eng JK, Moritz RL. Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Journal of Proteome Research. PMID 36648445 DOI: 10.1021/acs.jproteome.2c00624  0.334
2023 Hoopmann MR, Shteynberg DD, Zelter A, Riffle M, Lyon AS, Agard DA, Luan Q, Nolen BJ, MacCoss MJ, Davis TN, Moritz RL. Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline. Journal of Proteome Research. 22: 647-655. PMID 36629399 DOI: 10.1021/acs.jproteome.2c00670  0.361
2023 Kertesz-Farkas A, Nii Adoquaye Acquaye FL, Bhimani K, Eng JK, Fondrie WE, Grant C, Hoopmann MR, Lin A, Lu YY, Moritz RL, MacCoss MJ, Noble WS. The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Journal of Proteome Research. PMID 36598107 DOI: 10.1021/acs.jproteome.2c00615  0.418
2022 Riffle M, Hoopmann MR, Jaschob D, Zhong G, Moritz RL, MacCoss MJ, Davis TN, Isoherranen N, Zelter A. Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry. Analytical Chemistry. PMID 35184559 DOI: 10.1021/acs.analchem.1c04101  0.376
2021 Kailash V, Mendoza L, Moritz RL, Hoopmann MR. SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry. Journal of Proteome Research. PMID 33529024 DOI: 10.1021/acs.jproteome.0c00928  0.379
2020 Hoopmann MR, Kusebauch U, Palmblad M, Bandeira N, Shteynberg DD, He L, Xia B, Stoychev SH, Omenn GS, Weintraub ST, Moritz RL. Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. Journal of Proteome Research. PMID 33166149 DOI: 10.1021/acs.jproteome.0c00648  0.434
2020 Midha MK, Campbell DS, Kapil C, Kusebauch U, Hoopmann MR, Bader SL, Moritz RL. DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics. Nature Communications. 11: 5251. PMID 33067471 DOI: 10.1038/s41467-020-18901-y  0.393
2020 Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, et al. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure (London, England : 1993). PMID 33065067 DOI: 10.1016/j.str.2020.09.011  0.45
2019 Shteynberg DD, Deutsch EW, Campbell DS, Hoopmann MR, Kusebauch U, Lee D, Mendoza L, Midha MK, Sun Z, Whetton AD, Moritz RL. PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. Journal of Proteome Research. PMID 31290668 DOI: 10.1021/Acs.Jproteome.9B00205  0.496
2019 Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews PC, Bernfur K, Borchers CH, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis TN, ... ... Hoopmann MR, et al. The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study. Analytical Chemistry. PMID 31045356 DOI: 10.1021/Acs.Analchem.9B00658  0.674
2018 Slama P, Hoopmann MR, Moritz RL, Geman D. Robust determination of differential abundance in shotgun proteomics using nonparametric statistics. Molecular Omics. PMID 30259924 DOI: 10.1039/c8mo00077h  0.4
2018 Lee JY, Choi H, Colangelo CM, Davis D, Hoopmann MR, Käll L, Lam H, Payne SH, Perez-Riverol Y, The M, Wilson R, Weintraub ST, Palmblad M. ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data. Journal of Biomolecular Techniques : Jbt. PMID 29977167 DOI: 10.7171/Jbt.18-2902-003  0.405
2018 The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms. Journal of Proteome Research. PMID 29631402 DOI: 10.1021/Acs.Jproteome.7B00899  0.462
2018 Hoopmann MR, Winget JM, Mendoza L, Moritz RL. StPeter: Seamless label-free quantification with the Trans-Proteomic Pipeline. Journal of Proteome Research. PMID 29400476 DOI: 10.1021/Acs.Jproteome.7B00786  0.413
2016 Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O. ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments. Journal of Proteome Research. PMID 27990823 DOI: 10.1021/Acs.Jproteome.6B00881  0.561
2016 Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL. An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results. Journal of the American Society For Mass Spectrometry. PMID 27469004 DOI: 10.1007/S13361-016-1435-8  0.455
2016 Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. PMID 27453469 DOI: 10.1016/J.Cell.2016.06.041  0.405
2015 Swearingen KE, Winget JM, Hoopmann MR, Kusebauch U, Moritz RL. Decreased gap width in a cylindrical FAIMS device improves protein discovery. Analytical Chemistry. PMID 26560994 DOI: 10.1021/Acs.Analchem.5B03199  0.531
2015 Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN. The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling. Nature Communications. 6: 8673. PMID 26560693 DOI: 10.1038/Ncomms9673  0.519
2015 Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A. Testing and validation of computational methods for mass spectrometry. Journal of Proteome Research. PMID 26549429 DOI: 10.1021/Acs.Jproteome.5B00852  0.388
2015 Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra. Journal of the American Society For Mass Spectrometry. PMID 26419769 DOI: 10.1007/S13361-015-1252-5  0.468
2015 Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. A Deeper Look into Comet-Implementation and Features. Journal of the American Society For Mass Spectrometry. PMID 26115965 DOI: 10.1007/S13361-015-1179-X  0.73
2015 Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. Kojak: efficient analysis of chemically cross-linked protein complexes. Journal of Proteome Research. 14: 2190-8. PMID 25812159 DOI: 10.1021/Pr501321H  0.605
2014 Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR, MacCoss MJ, Moritz RL, Asbury CL, Davis TN. Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex. Genetics. 198: 1483-93. PMID 25230952 DOI: 10.1534/Genetics.114.167775  0.493
2014 McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS. Crux: rapid open source protein tandem mass spectrometry analysis. Journal of Proteome Research. 13: 4488-91. PMID 25182276 DOI: 10.1021/Pr500741Y  0.676
2013 Moruz L, Hoopmann MR, Rosenlund M, Granholm V, Moritz RL, Käll L. Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times. Journal of Proteome Research. 12: 5730-41. PMID 24074221 DOI: 10.1021/Pr400705Q  0.609
2013 Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE. Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research. Journal of Proteomics. 88: 109-19. PMID 23590889 DOI: 10.1016/J.Jprot.2013.04.009  0.426
2013 Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL. The state of the human proteome in 2012 as viewed through PeptideAtlas. Journal of Proteome Research. 12: 162-71. PMID 23215161 DOI: 10.1021/Pr301012J  0.495
2013 Eng JK, Jahan TA, Hoopmann MR. Comet: an open-source MS/MS sequence database search tool. Proteomics. 13: 22-4. PMID 23148064 DOI: 10.1002/Pmic.201200439  0.511
2013 Hoopmann MR, Moritz RL. Current algorithmic solutions for peptide-based proteomics data generation and identification. Current Opinion in Biotechnology. 24: 31-8. PMID 23142544 DOI: 10.1016/J.Copbio.2012.10.013  0.553
2012 Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J. Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. Bmc Bioinformatics. 13: 324. PMID 23216909 DOI: 10.1186/1471-2105-13-324  0.473
2012 Serang O, Moruz L, Hoopmann MR, Käll L. Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences. Journal of Proteome Research. 11: 5586-91. PMID 23148905 DOI: 10.1021/Pr300426S  0.4
2012 Hoopmann MR, MacCoss MJ, Moritz RL. Identification of peptide features in precursor spectra using hardklör and krönik Current Protocols in Bioinformatics. PMID 22389013 DOI: 10.1002/0471250953.Bi1318S37  0.692
2012 Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE. Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification. Journal of Proteome Research. 11: 1621-32. PMID 22288382 DOI: 10.1021/Pr2008175  0.549
2012 Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL. Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Molecular & Cellular Proteomics : McP. 11: M111.014985. PMID 22186714 DOI: 10.1074/Mcp.M111.014985  0.57
2012 Yang L, Zheng C, Weisbrod CR, Tang X, Munske GR, Hoopmann MR, Eng JK, Bruce JE. In vivo application of photocleavable protein interaction reporter technology. Journal of Proteome Research. 11: 1027-41. PMID 22168182 DOI: 10.1021/Pr200775J  0.41
2011 Hoopmann MR, Chavez JD, Bruce JE. SILACtor: software to enable dynamic SILAC studies. Analytical Chemistry. 83: 8403-10. PMID 21954881 DOI: 10.1021/Ac2017053  0.495
2011 Yang L, Vaitheesvaran B, Hartil K, Robinson AJ, Hoopmann MR, Eng JK, Kurland IJ, Bruce JE. The fasted/fed mouse metabolic acetylome: N6-acetylation differences suggest acetylation coordinates organ-specific fuel switching. Journal of Proteome Research. 10: 4134-49. PMID 21728379 DOI: 10.1021/Pr200313X  0.363
2011 Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE. Cross-linking measurements of in vivo protein complex topologies. Molecular & Cellular Proteomics : McP. 10: M110.006841. PMID 21697552 DOI: 10.1074/Mcp.M110.006841  0.383
2011 Dean MD, Findlay GD, Hoopmann MR, Wu CC, MacCoss MJ, Swanson WJ, Nachman MW. Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling. Bmc Genomics. 12: 306. PMID 21663664 DOI: 10.1186/1471-2164-12-306  0.546
2011 Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE. Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells. Plos One. 6: e19892. PMID 21637840 DOI: 10.1371/Journal.Pone.0019892  0.311
2010 Hoopmann MR, Weisbrod CR, Bruce JE. Improved strategies for rapid identification of chemically cross-linked peptides using protein interaction reporter technology. Journal of Proteome Research. 9: 6323-33. PMID 20886857 DOI: 10.1021/Pr100572U  0.543
2010 Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN. 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 Journal of Proteome Research. 9: 3583-3589. PMID 20476776 DOI: 10.1021/Pr1001115  0.655
2010 Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ. Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Analytical Chemistry. 82: 833-41. PMID 20039681 DOI: 10.1021/Ac901801B  0.783
2010 Hsieh EJ, Hoopmann MR, MacLean B, MacCoss MJ. Comparison of database search strategies for high precursor mass accuracy MS/MS data Journal of Proteome Research. 9: 1138-1143. PMID 19938873 DOI: 10.1021/Pr900816A  0.78
2009 Hoopmann MR, Merrihew GE, Von Haller PD, MacCoss MJ. Post analysis data acquisition for the Iterative MS/MS sampling of proteomics mixtures Journal of Proteome Research. 8: 1870-1875. PMID 19256536 DOI: 10.1021/Pr800828P  0.732
2008 Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ. Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics Analytical Chemistry. 80: 6888-6897. PMID 18693747 DOI: 10.1021/Ac8004988  0.735
2008 Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ. Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution μLC-MS data Analytical Chemistry. 80: 961-971. PMID 18189369 DOI: 10.1021/Ac701649E  0.759
2007 Hoopmann MR, Finney GL, MacCoss MJ. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Analytical Chemistry. 79: 5620-32. PMID 17580982 DOI: 10.1021/Ac0700833  0.785
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