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Items: 1 to 50 of 221

1.

The Micronemal Plasmodium Proteins P36 and P52 Act in Concert to Establish the Replication-Permissive Compartment Within Infected Hepatocytes.

Arredondo SA, Swearingen KE, Martinson T, Steel R, Dankwa DA, Harupa A, Camargo N, Betz W, Vigdorovich V, Oliver BG, Kangwanrangsan N, Ishino T, Sather N, Mikolajczak S, Vaughan AM, Torii M, Moritz RL, Kappe SHI.

Front Cell Infect Microbiol. 2018 Nov 27;8:413. doi: 10.3389/fcimb.2018.00413. eCollection 2018.

2.

A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry.

Swearingen KE, Eng JK, Shteynberg D, Vigdorovich V, Springer TA, Mendoza L, Sather DN, Deutsch EW, Kappe SHI, Moritz RL.

J Proteome Res. 2019 Feb 1;18(2):652-663. doi: 10.1021/acs.jproteome.8b00638. Epub 2018 Dec 21.

PMID:
30523691
3.

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
4.

Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.

Mendoza L, Deutsch EW, Sun Z, Campbell DS, Shteynberg DD, Moritz RL.

J Proteome Res. 2018 Sep 28. doi: 10.1021/acs.jproteome.8b00544. [Epub ahead of print]

PMID:
30230343
5.

A tissue-based draft map of the murine MHC class I immunopeptidome.

Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E.

Sci Data. 2018 Aug 7;5:180157. doi: 10.1038/sdata.2018.157.

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.

Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1.

Jabbari N, Glusman G, Joesch-Cohen LM, Reddy PJ, Moritz RL, Hood L, Lausted CG.

PLoS One. 2018 Jun 11;13(6):e0198135. doi: 10.1371/journal.pone.0198135. eCollection 2018.

8.

mRNA transcript distribution bias between Borrelia burgdorferi bacteria and their outer membrane vesicles.

Malge A, Ghai V, Reddy PJ, Baxter D, Kim TK, Moritz RL, Wang K.

FEMS Microbiol Lett. 2018 Jul 1;365(13). doi: 10.1093/femsle/fny135.

PMID:
29846577
9.

Selected reaction monitoring mass spectrometry of mastitis milk reveals pathogen-specific regulation of bovine host response proteins.

Kusebauch U, Hernández-Castellano LE, Bislev SL, Moritz RL, Røntved CM, Bendixen E.

J Dairy Sci. 2018 Jul;101(7):6532-6541. doi: 10.3168/jds.2017-14312. Epub 2018 Apr 11.

10.

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.

11.

RAD54 N-terminal domain is a DNA sensor that couples ATP hydrolysis with branch migration of Holliday junctions.

Goyal N, Rossi MJ, Mazina OM, Chi Y, Moritz RL, Clurman BE, Mazin AV.

Nat Commun. 2018 Jan 2;9(1):34. doi: 10.1038/s41467-017-02497-x.

12.

The SysteMHC Atlas project.

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.

13.

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW.

J Proteome Res. 2017 Dec 1;16(12):4299-4310. doi: 10.1021/acs.jproteome.7b00467. Epub 2017 Oct 10.

14.

A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.

Michalik S, Depke M, Murr A, Gesell Salazar M, Kusebauch U, Sun Z, Meyer TC, Surmann K, Pförtner H, Hildebrandt P, Weiss S, Palma Medina LM, Gutjahr M, Hammer E, Becher D, Pribyl T, Hammerschmidt S, Deutsch EW, Bader SL, Hecker M, Moritz RL, Mäder U, Völker U, Schmidt F.

Sci Rep. 2017 Sep 8;7(1):9718. doi: 10.1038/s41598-017-10059-w.

15.

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.

Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R.

Nat Commun. 2017 Aug 21;8(1):291. doi: 10.1038/s41467-017-00249-5.

16.

Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites.

Swearingen KE, Lindner SE, Flannery EL, Vaughan AM, Morrison RD, Patrapuvich R, Koepfli C, Muller I, Jex A, Moritz RL, Kappe SHI, Sattabongkot J, Mikolajczak SA.

PLoS Negl Trop Dis. 2017 Jul 31;11(7):e0005791. doi: 10.1371/journal.pntd.0005791. eCollection 2017 Jul.

17.

A wellness study of 108 individuals using personal, dense, dynamic data clouds.

Price ND, Magis AT, Earls JC, Glusman G, Levy R, Lausted C, McDonald DT, Kusebauch U, Moss CL, Zhou Y, Qin S, Moritz RL, Brogaard K, Omenn GS, Lovejoy JC, Hood L.

Nat Biotechnol. 2017 Aug;35(8):747-756. doi: 10.1038/nbt.3870. Epub 2017 Jul 17.

18.

The PeptideAtlas of the Domestic Laying Hen.

McCord J, Sun Z, Deutsch EW, Moritz RL, Muddiman DC.

J Proteome Res. 2017 Mar 3;16(3):1352-1363. doi: 10.1021/acs.jproteome.6b00952. Epub 2017 Feb 14.

19.

Building ProteomeTools based on a complete synthetic human proteome.

Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B.

Nat Methods. 2017 Mar;14(3):259-262. doi: 10.1038/nmeth.4153. Epub 2017 Jan 30.

20.

An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation.

Mandal K, Bader SL, Kumar P, Malakar D, Campbell DS, Pradhan BS, Sarkar RK, Wadhwa N, Sensharma S, Jain V, Moritz RL, Majumdar SS.

DNA Res. 2017 Apr 1;24(2):143-157. doi: 10.1093/dnares/dsw057.

21.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936. Epub 2016 Oct 18.

22.

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.

J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12.

23.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3961-3970. Epub 2016 Aug 24.

24.

Identification of Organ-Enriched Protein Biomarkers of Acute Liver Injury by Targeted Quantitative Proteomics of Blood in Acetaminophen- and Carbon-Tetrachloride-Treated Mouse Models and Acetaminophen Overdose Patients.

Qin S, Zhou Y, Gray L, Kusebauch U, McEvoy L, Antoine DJ, Hampson L, Park KB, Campbell D, Caballero J, Glusman G, Yan X, Kim TK, Yuan Y, Wang K, Rowen L, Moritz RL, Omenn GS, Pirmohamed M, Hood L.

J Proteome Res. 2016 Oct 7;15(10):3724-3740. Epub 2016 Sep 19.

PMID:
27575953
25.

An activated form of ADAM10 is tumor selective and regulates cancer stem-like cells and tumor growth.

Atapattu L, Saha N, Chheang C, Eissman MF, Xu K, Vail ME, Hii L, Llerena C, Liu Z, Horvay K, Abud HE, Kusebauch U, Moritz RL, Ding BS, Cao Z, Rafii S, Ernst M, Scott AM, Nikolov DB, Lackmann M, Janes PW.

J Exp Med. 2016 Aug 22;213(9):1741-57. doi: 10.1084/jem.20151095. Epub 2016 Aug 8.

26.

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.

27.

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.

28.

Interleukin-6 Induced "Acute" Phenotypic Microenvironment Promotes Th1 Anti-Tumor Immunity in Cryo-Thermal Therapy Revealed By Shotgun and Parallel Reaction Monitoring Proteomics.

Xue T, Liu P, Zhou Y, Liu K, Yang L, Moritz RL, Yan W, Xu LX.

Theranostics. 2016 Mar 21;6(6):773-94. doi: 10.7150/thno.14394. eCollection 2016.

29.

Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics.

Swearingen KE, Lindner SE, Shi L, Shears MJ, Harupa A, Hopp CS, Vaughan AM, Springer TA, Moritz RL, Kappe SH, Sinnis P.

PLoS Pathog. 2016 Apr 29;12(4):e1005606. doi: 10.1371/journal.ppat.1005606. eCollection 2016 Apr.

30.

Quantitative Proteomic Analysis of Stratum Corneum Dysfunction in Adult Chronic Atopic Dermatitis.

Winget JM, Finlay D, Mills KJ, Huggins T, Bascom C, Isfort RJ, Moritz RL.

J Invest Dermatol. 2016 Aug;136(8):1732-1735. doi: 10.1016/j.jid.2016.03.037. Epub 2016 Apr 14. No abstract available.

31.

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.

32.

Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.

Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M, Meyer MR, Qian WJ, Schoenherr RM, Scott MG, Shi T, Whiteley GR, Wrobel JA, Wu C, Ackermann BL, Aebersold R, Barnidge DR, Bunk DM, Clarke N, Fishman JB, Grant RP, Kusebauch U, Kushnir MM, Lowenthal MS, Moritz RL, Neubert H, Patterson SD, Rockwood AL, Rogers J, Singh RJ, Van Eyk JE, Wong SH, Zhang S, Chan DW, Chen X, Ellis MJ, Liebler DC, Rodland KD, Rodriguez H, Smith RD, Zhang Z, Zhang H, Paulovich AG.

Clin Chem. 2016 Jan;62(1):48-69. doi: 10.1373/clinchem.2015.250563.

33.

Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides.

Keller A, Bader SL, Kusebauch U, Shteynberg D, Hood L, Moritz RL.

Mol Cell Proteomics. 2016 Mar;15(3):1151-63. doi: 10.1074/mcp.M115.054478. Epub 2015 Dec 24.

34.

The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine.

Hesselager MO, Codrea MC, Sun Z, Deutsch EW, Bennike TB, Stensballe A, Bundgaard L, Moritz RL, Bendixen E.

Proteomics. 2016 Feb;16(4):634-44. doi: 10.1002/pmic.201500195.

35.

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.

36.

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.

37.

A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage.

Vialas V, Sun Z, Reales-Calderón JA, Hernáez ML, Casas V, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Moritz RL, Gil C.

J Proteomics. 2016 Jan 10;131:122-130. doi: 10.1016/j.jprot.2015.10.019. Epub 2015 Oct 19.

38.

RNA Sequencing Identifies Novel Translational Biomarkers of Kidney Fibrosis.

Craciun FL, Bijol V, Ajay AK, Rao P, Kumar RK, Hutchinson J, Hofmann O, Joshi N, Luyendyk JP, Kusebauch U, Moss CL, Srivastava A, Himmelfarb J, Waikar SS, Moritz RL, Vaidya VS.

J Am Soc Nephrol. 2016 Jun;27(6):1702-13. doi: 10.1681/ASN.2015020225. Epub 2015 Oct 8.

39.

The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.

Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, Tabb DL.

Mol Cell Proteomics. 2015 Dec;14(12):3299-309. doi: 10.1074/mcp.O115.051888. Epub 2015 Oct 4.

40.

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.

41.

A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.

Depke M, Michalik S, Rabe A, Surmann K, Brinkmann L, Jehmlich N, Bernhardt J, Hecker M, Wollscheid B, Sun Z, Moritz RL, Völker U, Schmidt F.

Proteomics. 2015 Nov;15(21):3648-61. doi: 10.1002/pmic.201500091. Epub 2015 Sep 7.

42.

An open-source computational and data resource to analyze digital maps of immunopeptidomes.

Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R.

Elife. 2015 Jul 8;4. doi: 10.7554/eLife.07661.

43.

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Deutsch EW, Sun Z, Campbell D, Kusebauch U, Chu CS, Mendoza L, Shteynberg D, Omenn GS, Moritz RL.

J Proteome Res. 2015 Sep 4;14(9):3461-73. doi: 10.1021/acs.jproteome.5b00500. Epub 2015 Jul 24.

44.

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.

45.

Correction for Zhang et al., The conserved SOCS box motif in suppressors of cytokine signaling binds to elongins B and C and may couple bound proteins to proteasomal degradation.

Zhang JG, Farley A, Nicholson SE, Willson TA, Zugaro LM, Simpson RJ, Moritz RL, Cary D, Richardson R, Hausmann G, Kile BT, Kent SB, Alexander WS, Metcalf D, Hilton DJ, Nicola NA, Baca M.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2979. doi: 10.1073/pnas.1507812112. Epub 2015 May 8. No abstract available.

46.

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.

47.

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.

48.

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet.

Keller A, Bader SL, Shteynberg D, Hood L, Moritz RL.

Mol Cell Proteomics. 2015 May;14(5):1411-8. doi: 10.1074/mcp.O114.044917. Epub 2015 Feb 24.

49.

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.

Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164. Epub 2015 Apr 2. Review.

50.

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.

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