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Items: 48

1.

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

Shteynberg DD, Deutsch EW, Campbell DS, Hoopmann MR, Kusebauch U, Lee D, Mendoza L, Midha MK, Sun Z, Whetton AD, Moritz RL.

J Proteome Res. 2019 Jul 10. doi: 10.1021/acs.jproteome.9b00205. [Epub ahead of print]

PMID:
31290668
2.

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

Pioner JM, Guan X, Klaiman JM, Racca AW, Pabon L, Muskheli V, Macadangdang J, Ferrantini C, Hoopmann MR, Moritz RL, Kim DH, Tesi C, Poggesi C, Murry CE, Childers MK, Mack DL, Regnier M.

Cardiovasc Res. 2019 May 2. pii: cvz109. doi: 10.1093/cvr/cvz109. [Epub ahead of print]

PMID:
31049579
3.

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

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A.

Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22.

4.

Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science.

Weintraub ST, Hoopmann MR, Palmblad M.

J Proteome Res. 2019 Feb 1;18(2):575. doi: 10.1021/acs.jproteome.9b00022. No abstract available.

PMID:
30704244
5.

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

Slama P, Hoopmann MR, Moritz RL, Geman D.

Mol Omics. 2018 Dec 3;14(6):424-436. doi: 10.1039/c8mo00077h.

PMID:
30259924
6.

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

Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, Kusebauch U, Sartain M, Guerriero G, O'Sullivan N, Teasdale M, Cipollini G, Paladin A, Mattiangeli V, Samadelli M, Tecchiati U, Putzer A, Palazoglu M, Meissen J, Lösch S, Rausch P, Baines JF, Kim BJ, An HJ, Gostner P, Egarter-Vigl E, Malfertheiner P, Keller A, Stark RW, Wenk M, Bishop D, Bradley DG, Fiehn O, Engstrand L, Moritz RL, Doble P, Franke A, Nebel A, Oeggl K, Rattei T, Grimm R, Zink A.

Curr Biol. 2018 Jul 23;28(14):2348-2355.e9. doi: 10.1016/j.cub.2018.05.067. Epub 2018 Jul 12.

7.

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

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.

J Biomol Tech. 2018 Jul;29(2):39-45. doi: 10.7171/jbt.18-2902-003. Epub 2018 Jun 21.

8.

A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms.

The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L.

J Proteome Res. 2018 May 4;17(5):1879-1886. doi: 10.1021/acs.jproteome.7b00899. Epub 2018 Apr 16.

9.

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

Hoopmann MR, Winget JM, Mendoza L, Moritz RL.

J Proteome Res. 2018 Mar 2;17(3):1314-1320. doi: 10.1021/acs.jproteome.7b00786. Epub 2018 Feb 14.

10.

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

Choi M, Eren-Dogu ZF, Colangelo C, Cottrell J, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O.

J Proteome Res. 2017 Feb 3;16(2):945-957. doi: 10.1021/acs.jproteome.6b00881. Epub 2017 Jan 3.

PMID:
27990823
11.

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

Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL.

J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. Epub 2016 Jul 28.

12.

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

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, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL.

Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21.

13.

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

Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, Kusebauch U, Vigl EE, Malfertheiner P, Megraud F, O'Sullivan N, Cipollini G, Coia V, Samadelli M, Engstrand L, Linz B, Moritz RL, Grimm R, Krause J, Nebel A, Moodley Y, Rattei T, Zink A.

Science. 2016 Jan 8;351(6269):162-165. doi: 10.1126/science.aad2545.

14.

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

Swearingen KE, Winget JM, Hoopmann MR, Kusebauch U, Moritz RL.

Anal Chem. 2015 Dec 15;87(24):12230-7. doi: 10.1021/acs.analchem.5b03199. Epub 2015 Nov 25.

15.

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

Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN.

Nat Commun. 2015 Nov 12;6:8673. doi: 10.1038/ncomms9673.

16.

Testing and Validation of Computational Methods for Mass Spectrometry.

Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A.

J Proteome Res. 2016 Mar 4;15(3):809-14. doi: 10.1021/acs.jproteome.5b00852. Epub 2015 Nov 17.

17.

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29.

18.

A deeper look into Comet--implementation and features.

Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1865-74. doi: 10.1007/s13361-015-1179-x. Epub 2015 Jun 27.

19.

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

Roume H, Heintz-Buschart A, Muller EEL, May P, Satagopam VP, Laczny CC, Narayanasamy S, Lebrun LA, Hoopmann MR, Schupp JM, Gillece JD, Hicks ND, Engelthaler DM, Sauter T, Keim PS, Moritz RL, Wilmes P.

NPJ Biofilms Microbiomes. 2015 Jun 17;1:15007. doi: 10.1038/npjbiofilms.2015.7. eCollection 2015.

20.

Quantitative proteogenomic profiling of epidermal barrier formation in vitro.

Winget JM, Watts JD, Hoopmann MR, DiColandrea T, Robinson MK, Huggins T, Bascom CC, Isfort RJ, Moritz RL.

J Dermatol Sci. 2015 Jun;78(3):173-80. doi: 10.1016/j.jdermsci.2015.02.013. Epub 2015 Mar 14.

21.

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

Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.

J Proteome Res. 2015 May 1;14(5):2190-8. doi: 10.1021/pr501321h. Epub 2015 Apr 15.

22.

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

Muller EE, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA, Roume H, Lin J, May P, Hicks ND, Heintz-Buschart A, Wampach L, Liu CM, Price LB, Gillece JD, Guignard C, Schupp JM, Vlassis N, Baliga NS, Moritz RL, Keim PS, Wilmes P.

Nat Commun. 2014 Nov 26;5:5603. doi: 10.1038/ncomms6603.

23.

Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex.

Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR 3rd, MacCoss MJ, Moritz RL, Asbury CL, Davis TN.

Genetics. 2014 Dec;198(4):1483-93. doi: 10.1534/genetics.114.167775. Epub 2014 Sep 16.

24.

Crux: rapid open source protein tandem mass spectrometry analysis.

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.

J Proteome Res. 2014 Oct 3;13(10):4488-91. doi: 10.1021/pr500741y. Epub 2014 Sep 9.

25.

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

Moruz L, Hoopmann MR, Rosenlund M, Granholm V, Moritz RL, Käll L.

J Proteome Res. 2013 Dec 6;12(12):5730-41. doi: 10.1021/pr400705q. Epub 2013 Oct 11.

26.

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

Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE.

J Proteomics. 2013 Aug 2;88:109-19. doi: 10.1016/j.jprot.2013.04.009. Epub 2013 Apr 13.

27.

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

Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.

BMC Bioinformatics. 2012 Dec 5;13:324. doi: 10.1186/1471-2105-13-324.

28.

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

Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL.

J Proteome Res. 2013 Jan 4;12(1):162-71. doi: 10.1021/pr301012j. Epub 2012 Dec 5.

29.

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

Serang O, Moruz L, Hoopmann MR, Käll L.

J Proteome Res. 2012 Dec 7;11(12):5586-91. doi: 10.1021/pr300426s. Epub 2012 Nov 19.

30.

Comet: an open-source MS/MS sequence database search tool.

Eng JK, Jahan TA, Hoopmann MR.

Proteomics. 2013 Jan;13(1):22-4. doi: 10.1002/pmic.201200439. Epub 2012 Dec 4.

PMID:
23148064
31.

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

Hoopmann MR, Moritz RL.

Curr Opin Biotechnol. 2013 Feb;24(1):31-8. doi: 10.1016/j.copbio.2012.10.013. Epub 2012 Nov 8. Review.

32.

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

Hoopmann MR, MacCoss MJ, Moritz RL.

Curr Protoc Bioinformatics. 2012 Mar;Chapter 13:Unit13.18. doi: 10.1002/0471250953.bi1318s37.

33.

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

Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.

J Proteome Res. 2012 Mar 2;11(3):1621-32. doi: 10.1021/pr2008175. Epub 2012 Feb 21.

34.

Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests.

Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL.

Mol Cell Proteomics. 2012 Apr;11(4):M111.014985. doi: 10.1074/mcp.M111.014985. Epub 2011 Dec 20.

35.

In vivo application of photocleavable protein interaction reporter technology.

Yang L, Zheng C, Weisbrod CR, Tang X, Munske GR, Hoopmann MR, Eng JK, Bruce JE.

J Proteome Res. 2012 Feb 3;11(2):1027-41. doi: 10.1021/pr200775j. Epub 2012 Jan 9.

36.

SILACtor: software to enable dynamic SILAC studies.

Hoopmann MR, Chavez JD, Bruce JE.

Anal Chem. 2011 Nov 15;83(22):8403-10. doi: 10.1021/ac2017053. Epub 2011 Oct 27.

37.

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

Yang L, Vaitheesvaran B, Hartil K, Robinson AJ, Hoopmann MR, Eng JK, Kurland IJ, Bruce JE.

J Proteome Res. 2011 Sep 2;10(9):4134-49. doi: 10.1021/pr200313x. Epub 2011 Aug 16.

38.

Cross-linking measurements of in vivo protein complex topologies.

Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE.

Mol Cell Proteomics. 2011 Oct;10(10):M110.006841. doi: 10.1074/mcp.M110.006841. Epub 2011 Jun 22.

39.

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

Dean MD, Findlay GD, Hoopmann MR, Wu CC, MacCoss MJ, Swanson WJ, Nachman MW.

BMC Genomics. 2011 Jun 10;12:306. doi: 10.1186/1471-2164-12-306.

40.

Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells.

Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE.

PLoS One. 2011;6(5):e19892. doi: 10.1371/journal.pone.0019892. Epub 2011 May 26.

41.

Improved strategies for rapid identification of chemically cross-linked peptides using protein interaction reporter technology.

Hoopmann MR, Weisbrod CR, Bruce JE.

J Proteome Res. 2010 Dec 3;9(12):6323-33. doi: 10.1021/pr100572u. Epub 2010 Nov 10.

42.
43.

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

Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ.

Anal Chem. 2010 Feb 1;82(3):833-41. doi: 10.1021/ac901801b.

44.

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

Hsieh EJ, Hoopmann MR, MacLean B, MacCoss MJ.

J Proteome Res. 2010 Feb 5;9(2):1138-43. doi: 10.1021/pr900816a.

45.

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

Hoopmann MR, Merrihew GE, von Haller PD, MacCoss MJ.

J Proteome Res. 2009 Apr;8(4):1870-5. doi: 10.1021/pr800828p.

46.

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

Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ.

Anal Chem. 2008 Sep 15;80(18):6888-97. doi: 10.1021/ac8004988. Epub 2008 Aug 12.

47.

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

Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ.

Anal Chem. 2008 Feb 15;80(4):961-71. doi: 10.1021/ac701649e. Epub 2008 Jan 12.

PMID:
18189369
48.

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