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Items: 48

1.

Selection of Heating Temperatures Improves the Sensitivity of Proteome Integral Solubility Alteration (PISA) Assay.

Li J, Van Vranken JG, Paulo JA, Huttlin EL, Gygi SP.

J Proteome Res. 2020 Apr 3. doi: 10.1021/acs.jproteome.0c00063. [Epub ahead of print]

PMID:
32243163
2.

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples.

Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, Paulo JA.

Nat Methods. 2020 Apr;17(4):399-404. doi: 10.1038/s41592-020-0781-4. Epub 2020 Mar 16.

PMID:
32203386
3.

Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics.

Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP.

J Proteome Res. 2020 Apr 6. doi: 10.1021/acs.jproteome.9b00860. [Epub ahead of print]

PMID:
32126768
4.

A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging.

Xiao H, Jedrychowski MP, Schweppe DK, Huttlin EL, Yu Q, Heppner DE, Li J, Long J, Mills EL, Szpyt J, He Z, Du G, Garrity R, Reddy A, Vaites LP, Paulo JA, Zhang T, Gray NS, Gygi SP, Chouchani ET.

Cell. 2020 Mar 5;180(5):968-983.e24. doi: 10.1016/j.cell.2020.02.012. Epub 2020 Feb 27.

PMID:
32109415
5.

Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions.

Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP.

Elife. 2019 Dec 24;8. pii: e49894. doi: 10.7554/eLife.49894.

6.

Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast.

Li J, Paulo JA, Nusinow DP, Huttlin EL, Gygi SP.

Cell Rep. 2019 Nov 12;29(7):2092-2104.e4. doi: 10.1016/j.celrep.2019.10.034.

7.

High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms.

Nightingale K, Lin KM, Ravenhill BJ, Davies C, Nobre L, Fielding CA, Ruckova E, Fletcher-Etherington A, Soday L, Nichols H, Sugrue D, Wang ECY, Moreno P, Umrania Y, Huttlin EL, Antrobus R, Davison AJ, Wilkinson GWG, Stanton RJ, Tomasec P, Weekes MP.

Cell Host Microbe. 2018 Sep 12;24(3):447-460.e11. doi: 10.1016/j.chom.2018.07.011. Epub 2018 Aug 16.

8.

Characterization of Plasmodium falciparum Atypical Kinase PfPK7- Dependent Phosphoproteome.

Pease BN, Huttlin EL, Jedrychowski MP, Dorin-Semblat D, Sebastiani D, Segarra DT, Roberts BF, Chakrabarti R, Doerig C, Gygi SP, Chakrabarti D.

J Proteome Res. 2018 Jun 1;17(6):2112-2123. doi: 10.1021/acs.jproteome.8b00062. Epub 2018 Apr 30.

PMID:
29678115
9.

DNAJC12: A molecular chaperone involved in proteostasis, PKU, biogenic amines metabolism and beyond?

Bouchereau J, Huttlin EL, Guarani V, Pichard S, Anikster Y, Schiff M.

Mol Genet Metab. 2018 Mar;123(3):285-286. doi: 10.1016/j.ymgme.2018.01.006. Epub 2018 Feb 12. No abstract available.

PMID:
29396030
10.

Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags.

O'Brien JJ, O'Connell JD, Paulo JA, Thakurta S, Rose CM, Weekes MP, Huttlin EL, Gygi SP.

J Proteome Res. 2018 Jan 5;17(1):590-599. doi: 10.1021/acs.jproteome.7b00699. Epub 2017 Dec 15.

11.

BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data.

Schweppe DK, Huttlin EL, Harper JW, Gygi SP.

J Proteome Res. 2018 Jan 5;17(1):722-726. doi: 10.1021/acs.jproteome.7b00572. Epub 2017 Oct 31.

12.

Systematic Analysis of Human Cells Lacking ATG8 Proteins Uncovers Roles for GABARAPs and the CCZ1/MON1 Regulator C18orf8/RMC1 in Macroautophagic and Selective Autophagic Flux.

Vaites LP, Paulo JA, Huttlin EL, Harper JW.

Mol Cell Biol. 2017 Dec 13;38(1). pii: e00392-17. doi: 10.1128/MCB.00392-17. Print 2018 Jan 1.

13.

Architecture of the human interactome defines protein communities and disease networks.

Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, White AE, Schweppe DK, Rad R, Erickson BK, Obar RA, Guruharsha KG, Li K, Artavanis-Tsakonas S, Gygi SP, Harper JW.

Nature. 2017 May 25;545(7655):505-509. doi: 10.1038/nature22366. Epub 2017 May 17.

14.

Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability.

Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thöny B, Shen N, Guarani V, Meissner T, Mayatepek E, Trefz FK, Marek-Yagel D, Martinez A, Huttlin EL, Paulo JA, Berutti R, Benoist JF, Imbard A, Dorboz I, Heimer G, Landau Y, Ziv-Strasser L, Malicdan MCV, Gemperle-Britschgi C, Cremer K, Engels H, Meili D, Keller I, Bruggmann R, Strom TM, Meitinger T, Mullikin JC, Schwartz G, Ben-Zeev B, Gahl WA, Harper JW, Blau N, Hoffmann GF, Prokisch H, Opladen T, Schiff M.

Am J Hum Genet. 2017 Feb 2;100(2):257-266. doi: 10.1016/j.ajhg.2017.01.002. Epub 2017 Jan 26.

15.

Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags.

Everley RA, Huttlin EL, Erickson AR, Beausoleil SA, Gygi SP.

J Proteome Res. 2017 Feb 3;16(2):1069-1076. doi: 10.1021/acs.jproteome.6b00487. Epub 2016 Dec 30.

16.

Defining the consequences of genetic variation on a proteome-wide scale.

Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP.

Nature. 2016 Jun 23;534(7608):500-5. doi: 10.1038/nature18270. Epub 2016 Jun 15.

17.

Corrigendum: Systematic proteomics of the VCP-UBXD adaptor network identifies a role for UBXN10 in regulating ciliogenesis.

Raman M, Sergeev M, Garnaas M, Lydeard JR, Huttlin EL, Goessling W, Shah JV, Harper JW.

Nat Cell Biol. 2016 Mar;18(3):347. doi: 10.1038/ncb3318. No abstract available.

PMID:
26911913
18.

Systematic proteomics of the VCP-UBXD adaptor network identifies a role for UBXN10 in regulating ciliogenesis.

Raman M, Sergeev M, Garnaas M, Lydeard JR, Huttlin EL, Goessling W, Shah JV, Harper JW.

Nat Cell Biol. 2015 Oct;17(10):1356-69. doi: 10.1038/ncb3238. Epub 2015 Sep 21. Erratum in: Nat Cell Biol. 2016 Mar;18(3):347.

19.

Erratum: A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.

Chick JM, Kolippakkam D, Nusinow DP, Zhai B, Rad R, Huttlin EL, Gygi SP.

Nat Biotechnol. 2015 Aug;33(8):882. doi: 10.1038/nbt0815-882d. No abstract available.

PMID:
26252148
20.

The BioPlex Network: A Systematic Exploration of the Human Interactome.

Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP.

Cell. 2015 Jul 16;162(2):425-440. doi: 10.1016/j.cell.2015.06.043.

21.

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.

Chick JM, Kolippakkam D, Nusinow DP, Zhai B, Rad R, Huttlin EL, Gygi SP.

Nat Biotechnol. 2015 Jul;33(7):743-9. doi: 10.1038/nbt.3267. Epub 2015 Jun 15. Erratum in: Nat Biotechnol. 2015 Aug;33(8):882. Erratum in: Nat Biotechnol. 2015 Aug;33(8):882.

22.

Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response.

Elia AE, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ.

Mol Cell. 2015 Sep 3;59(5):867-81. doi: 10.1016/j.molcel.2015.05.006. Epub 2015 Jun 4.

23.

QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology.

Guarani V, McNeill EM, Paulo JA, Huttlin EL, Fröhlich F, Gygi SP, Van Vactor D, Harper JW.

Elife. 2015 May 21;4. doi: 10.7554/eLife.06265.

24.

MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes.

McAlister GC, Nusinow DP, Jedrychowski MP, Wühr M, Huttlin EL, Erickson BK, Rad R, Haas W, Gygi SP.

Anal Chem. 2014 Jul 15;86(14):7150-8. doi: 10.1021/ac502040v. Epub 2014 Jul 3.

25.

Quantitative temporal viromics: an approach to investigate host-pathogen interaction.

Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang EC, Aicheler R, Murrell I, Wilkinson GW, Lehner PJ, Gygi SP.

Cell. 2014 Jun 5;157(6):1460-72. doi: 10.1016/j.cell.2014.04.028.

26.

Proteomic analysis of cap-dependent translation identifies LARP1 as a key regulator of 5'TOP mRNA translation.

Tcherkezian J, Cargnello M, Romeo Y, Huttlin EL, Lavoie G, Gygi SP, Roux PP.

Genes Dev. 2014 Feb 15;28(4):357-71. doi: 10.1101/gad.231407.113.

27.

TIMMDC1/C3orf1 functions as a membrane-embedded mitochondrial complex I assembly factor through association with the MCIA complex.

Guarani V, Paulo J, Zhai B, Huttlin EL, Gygi SP, Harper JW.

Mol Cell Biol. 2014 Mar;34(5):847-61. doi: 10.1128/MCB.01551-13. Epub 2013 Dec 16.

28.

Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the ApcMin/+ mouse.

Ivancic MM, Huttlin EL, Chen X, Pleiman JK, Irving AA, Hegeman AD, Dove WF, Sussman MR.

J Proteome Res. 2013 Sep 6;12(9):4152-66. doi: 10.1021/pr400467c. Epub 2013 Aug 8.

29.

Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development.

Pease BN, Huttlin EL, Jedrychowski MP, Talevich E, Harmon J, Dillman T, Kannan N, Doerig C, Chakrabarti R, Gygi SP, Chakrabarti D.

J Proteome Res. 2013 Sep 6;12(9):4028-45. doi: 10.1021/pr400394g. Epub 2013 Aug 26.

30.

Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.

Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.

Nature. 2013 Apr 18;496(7445):372-6. doi: 10.1038/nature12043. Epub 2013 Mar 17.

31.

Gab2 phosphorylation by RSK inhibits Shp2 recruitment and cell motility.

Zhang X, Lavoie G, Fort L, Huttlin EL, Tcherkezian J, Galan JA, Gu H, Gygi SP, Carreno S, Roux PP.

Mol Cell Biol. 2013 Apr;33(8):1657-70. doi: 10.1128/MCB.01353-12. Epub 2013 Feb 11.

32.

Phosphorylation of the eukaryotic translation initiation factor 4E-transporter (4E-T) by c-Jun N-terminal kinase promotes stress-dependent P-body assembly.

Cargnello M, Tcherkezian J, Dorn JF, Huttlin EL, Maddox PS, Gygi SP, Roux PP.

Mol Cell Biol. 2012 Nov;32(22):4572-84. doi: 10.1128/MCB.00544-12. Epub 2012 Sep 10.

33.

Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses.

McAlister GC, Huttlin EL, Haas W, Ting L, Jedrychowski MP, Rogers JC, Kuhn K, Pike I, Grothe RA, Blethrow JD, Gygi SP.

Anal Chem. 2012 Sep 4;84(17):7469-78. doi: 10.1021/ac301572t. Epub 2012 Aug 20.

34.

Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics.

Jedrychowski MP, Huttlin EL, Haas W, Sowa ME, Rad R, Gygi SP.

Mol Cell Proteomics. 2011 Dec;10(12):M111.009910. doi: 10.1074/mcp.M111.009910. Epub 2011 Sep 13.

35.

Systematic and quantitative assessment of the ubiquitin-modified proteome.

Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.

Mol Cell. 2011 Oct 21;44(2):325-40. doi: 10.1016/j.molcel.2011.08.025. Epub 2011 Sep 8.

36.

A large-scale method to measure absolute protein phosphorylation stoichiometries.

Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP.

Nat Methods. 2011 Jul 3;8(8):677-83. doi: 10.1038/nmeth.1636.

37.

Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes.

Wu R, Dephoure N, Haas W, Huttlin EL, Zhai B, Sowa ME, Gygi SP.

Mol Cell Proteomics. 2011 Aug;10(8):M111.009654. doi: 10.1074/mcp.M111.009654. Epub 2011 May 7.

38.

A tissue-specific atlas of mouse protein phosphorylation and expression.

Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP.

Cell. 2010 Dec 23;143(7):1174-89. doi: 10.1016/j.cell.2010.12.001.

39.

Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution.

Huttlin EL, Chen X, Barrett-Wilt GA, Hegeman AD, Halberg RB, Harms AC, Newton MA, Dove WF, Sussman MR.

Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17235-40. doi: 10.1073/pnas.0909282106. Epub 2009 Sep 23.

40.

Democratization and integration of genomic profiling tools.

Sussman MR, Huttlin EL, Wohlbach DJ.

Methods Mol Biol. 2009;553:373-93. doi: 10.1007/978-1-60327-563-7_20. Review.

PMID:
19588117
41.

Matching isotopic distributions from metabolically labeled samples.

McIlwain S, Page D, Huttlin EL, Sussman MR.

Bioinformatics. 2008 Jul 1;24(13):i339-47. doi: 10.1093/bioinformatics/btn190.

42.

Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses.

Mock T, Samanta MP, Iverson V, Berthiaume C, Robison M, Holtermann K, Durkin C, Bondurant SS, Richmond K, Rodesch M, Kallas T, Huttlin EL, Cerrina F, Sussman MR, Armbrust EV.

Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1579-84. doi: 10.1073/pnas.0707946105. Epub 2008 Jan 22.

43.

Stable isotope assisted assignment of elemental compositions for metabolomics.

Hegeman AD, Schulte CF, Cui Q, Lewis IA, Huttlin EL, Eghbalnia H, Harms AC, Ulrich EL, Markley JL, Sussman MR.

Anal Chem. 2007 Sep 15;79(18):6912-21. Epub 2007 Aug 21.

PMID:
17708672
44.

Using dynamic programming to create isotopic distribution maps from mass spectra.

McIlwain S, Page D, Huttlin EL, Sussman MR.

Bioinformatics. 2007 Jul 1;23(13):i328-36.

PMID:
17646314
45.

Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana.

Nelson CJ, Huttlin EL, Hegeman AD, Harms AC, Sussman MR.

Proteomics. 2007 Apr;7(8):1279-92.

PMID:
17443642
46.

Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana.

Huttlin EL, Hegeman AD, Harms AC, Sussman MR.

Mol Cell Proteomics. 2007 May;6(5):860-81. Epub 2007 Feb 9.

48.

A transcriptome-based characterization of habituation in plant tissue culture.

Pischke MS, Huttlin EL, Hegeman AD, Sussman MR.

Plant Physiol. 2006 Apr;140(4):1255-78. Epub 2006 Feb 17. Erratum in: Plant Physiol. 2009 Sep;151(1):479.

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