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Items: 1 to 50 of 337

1.

Rapamycin persistently improves cardiac function in aged, male and female mice, even following cessation of treatment.

Quarles E, Basisty N, Chiao YA, Merrihew G, Gu H, Sweetwyne MT, Fredrickson J, Nguyen NH, Razumova M, Kooiker K, Moussavi-Harami F, Regnier M, Quarles C, MacCoss M, Rabinovitch PS.

Aging Cell. 2019 Dec 10:e13086. doi: 10.1111/acel.13086. [Epub ahead of print]

2.

Assessing protein sequence database suitability using de novo sequencing.

Johnson R, Searle BC, Nunn BL, Gilmore JM, Phillips M, Amemiya CT, Heck M, MacCoss MJ.

Mol Cell Proteomics. 2019 Nov 15. pii: mcp.TIR119.001752. doi: 10.1074/mcp.TIR119.001752. [Epub ahead of print]

3.

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA.

Nucleic Acids Res. 2019 Nov 5. pii: gkz984. doi: 10.1093/nar/gkz984. [Epub ahead of print]

PMID:
31686107
4.

Differential effects of various genetic mouse models of the mechanistic target of rapamycin complex I inhibition on heart failure.

Dai DF, Liu Y, Basisty N, Karunadharma P, Dastidar SG, Chiao YA, Chen T, Beyer RP, Chin MT, Maccoss M, La Spada AR, Rabinovitch PS.

Geroscience. 2019 Oct 24. doi: 10.1007/s11357-019-00119-6. [Epub ahead of print]

PMID:
31650481
5.

Kinetochore-associated Stu2 promotes chromosome biorientation in vivo.

Miller MP, Evans RK, Zelter A, Geyer EA, MacCoss MJ, Rice LM, Davis TN, Asbury CL, Biggins S.

PLoS Genet. 2019 Oct 4;15(10):e1008423. doi: 10.1371/journal.pgen.1008423. eCollection 2019 Oct.

6.

Thesaurus: quantifying phosphopeptide positional isomers.

Searle BC, Lawrence RT, MacCoss MJ, Villén J.

Nat Methods. 2019 Aug;16(8):703-706. doi: 10.1038/s41592-019-0498-4. Epub 2019 Jul 29.

PMID:
31363206
7.

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.

8.

Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective.

Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ.

Autophagy. 2019 Sep;15(9):1592-1605. doi: 10.1080/15548627.2019.1586258. Epub 2019 Mar 21.

PMID:
30865561
9.

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.

Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ.

J Am Soc Mass Spectrom. 2019 Apr;30(4):669-684. doi: 10.1007/s13361-018-2122-8. Epub 2019 Jan 22.

10.

Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL.

Mol Cell Proteomics. 2019 Jan;18(1):1-2. doi: 10.1074/mcp.E118.001286. No abstract available.

11.

Improving mitochondrial function with SS-31 reverses age-related redox stress and improves exercise tolerance in aged mice.

Campbell MD, Duan J, Samuelson AT, Gaffrey MJ, Merrihew GE, Egertson JD, Wang L, Bammler TK, Moore RJ, White CC, Kavanagh TJ, Voss JG, Szeto HH, Rabinovitch PS, MacCoss MJ, Qian WJ, Marcinek DJ.

Free Radic Biol Med. 2019 Apr;134:268-281. doi: 10.1016/j.freeradbiomed.2018.12.031. Epub 2018 Dec 28.

PMID:
30597195
12.

Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis.

Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ.

FEBS Lett. 2019 Feb;593(3):319-338. doi: 10.1002/1873-3468.13311. Epub 2018 Dec 28.

13.

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry.

Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villén J, MacCoss MJ.

Nat Commun. 2018 Dec 3;9(1):5128. doi: 10.1038/s41467-018-07454-w.

14.

Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics.

Kim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, Woo S, Liao WL, Merrihew GE, Searle BC, Vaske C, Heaton R, MacCoss MJ, Hembrough T.

J Proteome Res. 2019 Jan 4;18(1):426-435. doi: 10.1021/acs.jproteome.8b00699. Epub 2018 Dec 12.

PMID:
30481034
15.

The Interaction Dynamics of Two Potato Leafroll Virus Movement Proteins Affects Their Localization to the Outer Membranes of Mitochondria and Plastids.

DeBlasio SL, Xu Y, Johnson RS, Rebelo AR, MacCoss MJ, Gray SM, Heck M.

Viruses. 2018 Oct 26;10(11). pii: E585. doi: 10.3390/v10110585.

16.

Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories.

Pino LK, Searle BC, Huang EL, Noble WS, Hoofnagle AN, MacCoss MJ.

Anal Chem. 2018 Nov 6;90(21):13112-13117. doi: 10.1021/acs.analchem.8b04581. Epub 2018 Oct 23.

17.

Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles.

Thomas RE, Vincow ES, Merrihew GE, MacCoss MJ, Davis MY, Pallanck LJ.

PLoS Genet. 2018 Sep 26;14(9):e1007694. doi: 10.1371/journal.pgen.1007694. eCollection 2018 Sep.

18.

Candidatus Liberibacter asiaticus Minimally Alters Expression of Immunity and Metabolism Proteins in Hemolymph of Diaphorina citri, the Insect Vector of Huanglongbing.

Kruse A, Ramsey JS, Johnson R, Hall DG, MacCoss MJ, Heck M.

J Proteome Res. 2018 Sep 7;17(9):2995-3011. doi: 10.1021/acs.jproteome.8b00183. Epub 2018 Aug 27.

PMID:
30106293
19.

Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions.

MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES.

J Am Soc Mass Spectrom. 2018 Nov;29(11):2182-2188. doi: 10.1007/s13361-018-2028-5. Epub 2018 Jul 25.

20.

Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems.

Claw KG, George RD, MacCoss MJ, Swanson WJ.

BMC Genomics. 2018 Jun 22;19(1):488. doi: 10.1186/s12864-018-4872-x.

21.

Novel phosphorylation states of the yeast spindle pole body.

Fong KK, Zelter A, Graczyk B, Hoyt JM, Riffle M, Johnson R, MacCoss MJ, Davis TN.

Biol Open. 2018 Oct 8;7(10). pii: bio033647. doi: 10.1242/bio.033647.

22.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

Litichevskiy L, Peckner R, Abelin JG, Asiedu JK, Creech AL, Davis JF, Davison D, Dunning CM, Egertson JD, Egri S, Gould J, Ko T, Johnson SA, Lahr DL, Lam D, Liu Z, Lyons NJ, Lu X, MacLean BX, Mungenast AE, Officer A, Natoli TE, Papanastasiou M, Patel J, Sharma V, Toder C, Tubelli AA, Young JZ, Carr SA, Golub TR, Subramanian A, MacCoss MJ, Tsai LH, Jaffe JD.

Cell Syst. 2018 Apr 25;6(4):424-443.e7. doi: 10.1016/j.cels.2018.03.012. Epub 2018 Apr 11.

23.

A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack.

Tseng BS, Reichhardt C, Merrihew GE, Araujo-Hernandez SA, Harrison JJ, MacCoss MJ, Parsek MR.

MBio. 2018 Apr 10;9(2). pii: e00543-18. doi: 10.1128/mBio.00543-18.

24.

Direct sulfonylation of anilines mediated by visible light.

Johnson TC, Elbert BL, Farley AJM, Gorman TW, Genicot C, Lallemand B, Pasau P, Flasz J, Castro JL, MacCoss M, Dixon DJ, Paton RS, Schofield CJ, Smith MD, Willis MC.

Chem Sci. 2017 Nov 16;9(3):629-633. doi: 10.1039/c7sc03891g. eCollection 2018 Jan 21.

25.

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics.

Peckner R, Myers SA, Jacome ASV, Egertson JD, Abelin JG, MacCoss MJ, Carr SA, Jaffe JD.

Nat Methods. 2018 May;15(5):371-378. doi: 10.1038/nmeth.4643. Epub 2018 Apr 2.

26.

A Stem-Loop Structure in Potato Leafroll Virus Open Reading Frame 5 (ORF5) Is Essential for Readthrough Translation of the Coat Protein ORF Stop Codon 700 Bases Upstream.

Xu Y, Ju HJ, DeBlasio S, Carino EJ, Johnson R, MacCoss MJ, Heck M, Miller WA, Gray SM.

J Virol. 2018 May 14;92(11). pii: e01544-17. doi: 10.1128/JVI.01544-17. Print 2018 Jun 1.

27.

Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments.

Helgeson LA, Zelter A, Riffle M, MacCoss MJ, Asbury CL, Davis TN.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2740-2745. doi: 10.1073/pnas.1718553115. Epub 2018 Feb 27.

28.

Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.

Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B.

Mol Cell Proteomics. 2018 Jun;17(6):1239-1244. doi: 10.1074/mcp.RA117.000543. Epub 2018 Feb 27.

29.

How many human proteoforms are there?

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.

30.

Nonlinear Regression Improves Accuracy of Characterization of Multiplexed Mass Spectrometric Assays.

Galitzine C, Egertson JD, Abbatiello S, Henderson CM, Pino LK, MacCoss M, Hoofnagle AN, Vitek O.

Mol Cell Proteomics. 2018 May;17(5):913-924. doi: 10.1074/mcp.RA117.000322. Epub 2018 Feb 9.

31.

Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex.

Luan Q, Zelter A, MacCoss MJ, Davis TN, Nolen BJ.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1409-E1418. doi: 10.1073/pnas.1716622115. Epub 2018 Jan 31.

32.

Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin.

Henderson CM, Shulman NJ, MacLean B, MacCoss MJ, Hoofnagle AN.

Clin Chem. 2018 Feb;64(2):408-410. doi: 10.1373/clinchem.2017.282293. Epub 2017 Dec 4. No abstract available.

33.

Importance of Rigidity in Designing Small Molecule Drugs To Tackle Protein-Protein Interactions (PPIs) through Stabilization of Desired Conformers.

Lawson ADG, MacCoss M, Heer JP.

J Med Chem. 2018 May 24;61(10):4283-4289. doi: 10.1021/acs.jmedchem.7b01120. Epub 2017 Nov 28.

34.

DnaJ Homolog Subfamily B Member 9 Is a Putative Autoantigen in Fibrillary GN.

Andeen NK, Yang HY, Dai DF, MacCoss MJ, Smith KD.

J Am Soc Nephrol. 2018 Jan;29(1):231-239. doi: 10.1681/ASN.2017050566. Epub 2017 Nov 2.

35.

Stable Isotope Labeling Reveals Novel Insights Into Ubiquitin-Mediated Protein Aggregation With Age, Calorie Restriction, and Rapamycin Treatment.

Basisty NB, Liu Y, Reynolds J, Karunadharma PP, Dai DF, Fredrickson J, Beyer RP, MacCoss MJ, Rabinovitch PS.

J Gerontol A Biol Sci Med Sci. 2018 Apr 17;73(5):561-570. doi: 10.1093/gerona/glx047.

36.

C-H Cyanation of 6-Ring N-Containing Heteroaromatics.

Elbert BL, Farley AJM, Gorman TW, Johnson TC, Genicot C, Lallemand B, Pasau P, Flasz J, Castro JL, MacCoss M, Paton RS, Schofield CJ, Smith MD, Willis MC, Dixon DJ.

Chemistry. 2017 Oct 20;23(59):14733-14737. doi: 10.1002/chem.201703931. Epub 2017 Sep 22.

37.

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.

Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R.

Nat Methods. 2017 Sep;14(9):921-927. doi: 10.1038/nmeth.4398. Epub 2017 Aug 21.

38.

Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry.

DeBlasio SL, Bereman MS, Mahoney J, Thannhauser TW, Gray SM, MacCoss MJ, Cilia Heck M.

J Biomol Tech. 2017 Sep;28(3):111-121. doi: 10.7171/jbt.17-2803-002. Epub 2017 Jul 24.

39.

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.

Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ.

Nat Methods. 2017 Sep;14(9):903-908. doi: 10.1038/nmeth.4390. Epub 2017 Aug 7.

40.

Development of Selected Reaction Monitoring Methods to Systematically Quantify Kinase Abundance and Phosphorylation Stoichiometry in Human Samples.

Beck K, Camp N, Bereman M, Bollinger J, Egertson J, MacCoss M, Wolf-Yadlin A.

Methods Mol Biol. 2017;1636:353-369. doi: 10.1007/978-1-4939-7154-1_23.

PMID:
28730491
41.

A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain.

Goulding SP, Szumlinski KK, Contet C, MacCoss MJ, Wu CC.

J Proteomics. 2017 Aug 23;166:127-137. doi: 10.1016/j.jprot.2017.07.008. Epub 2017 Jul 17.

42.

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.

Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ.

Mass Spectrom Rev. 2017 Jul 9. doi: 10.1002/mas.21540. [Epub ahead of print] Review.

43.

Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein.

Sakano H, Zorio DAR, Wang X, Ting YS, Noble WS, MacCoss MJ, Rubel EW, Wang Y.

J Comp Neurol. 2017 Oct 15;525(15):3341-3359. doi: 10.1002/cne.24281. Epub 2017 Jul 24.

44.

Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut.

Kruse A, Fattah-Hosseini S, Saha S, Johnson R, Warwick E, Sturgeon K, Mueller L, MacCoss MJ, Shatters RG Jr, Cilia Heck M.

PLoS One. 2017 Jun 20;12(6):e0179531. doi: 10.1371/journal.pone.0179531. eCollection 2017.

45.

TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis.

Kubota A, Ito S, Shim JS, Johnson RS, Song YH, Breton G, Goralogia GS, Kwon MS, Laboy Cintrón D, Koyama T, Ohme-Takagi M, Pruneda-Paz JL, Kay SA, MacCoss MJ, Imaizumi T.

PLoS Genet. 2017 Jun 19;13(6):e1006856. doi: 10.1371/journal.pgen.1006856. eCollection 2017 Jun.

46.

Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube Morphogenesis Defects in Drosophila melanogaster.

Zimmerman SG, Merrihew GE, MacCoss MJ, Berg CA.

Genetics. 2017 Jun;206(2):973-984. doi: 10.1534/genetics.116.199323. Epub 2017 Apr 12.

47.

Protein interaction networks at the host-microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen.

Ramsey JS, Chavez JD, Johnson R, Hosseinzadeh S, Mahoney JE, Mohr JP, Robison F, Zhong X, Hall DG, MacCoss M, Bruce J, Cilia M.

R Soc Open Sci. 2017 Feb 8;4(2):160545. doi: 10.1098/rsos.160545. eCollection 2017 Feb.

48.

Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography.

Spencer SE, Corso TN, Bollinger JG, Henderson CM, Hoofnagle AN, MacCoss MJ.

Anal Chem. 2017 Feb 21;89(4):2383-2389. doi: 10.1021/acs.analchem.6b04227. Epub 2017 Jan 30.

49.

The Ndc80 complex bridges two Dam1 complex rings.

Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN.

Elife. 2017 Feb 13;6. pii: e21069. doi: 10.7554/eLife.21069.

50.

New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.

Abbatiello S, Ackermann BL, Borchers C, Bradshaw RA, Carr SA, Chalkley R, Choi M, Deutsch E, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss M, MacLean B, Mani DR, Neubert H, Smith D, Vitek O, Zimmerman L.

Mol Cell Proteomics. 2017 Mar;16(3):327-328. doi: 10.1074/mcp.E117.067801. Epub 2017 Feb 9. No abstract available.

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