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Items: 21

1.

Pacific geoduck (Panopea generosa) resilience to natural pH variation.

Spencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB.

Comp Biochem Physiol Part D Genomics Proteomics. 2019 Jun;30:91-101. doi: 10.1016/j.cbd.2019.01.010. Epub 2019 Jan 24.

PMID:
30818101
2.

Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.

Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ 4th, Hettich RL, Jagtap PD, Janech MG, Kinkade DB, Leary DH, McIlvin MR, Moore EK, Morris RM, Neely BA, Nunn BL, Saunders JK, Shepherd AI, Symmonds NI, Walsh DA.

J Proteome Res. 2019 Apr 5;18(4):1461-1476. doi: 10.1021/acs.jproteome.8b00761. Epub 2019 Mar 12.

PMID:
30702898
3.

MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides.

Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL.

Sci Rep. 2018 Jun 18;8(1):9276. doi: 10.1038/s41598-018-27650-4.

4.

MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data.

Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jaschob D, Noble WS, Nunn BL.

Proteomes. 2017 Dec 27;6(1). pii: E2. doi: 10.3390/proteomes6010002.

5.

Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome.

Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S.

J Proteomics. 2018 Feb 20;173:89-98. doi: 10.1016/j.jprot.2017.11.025. Epub 2017 Dec 5.

PMID:
29208510
6.

Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation.

Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB.

J Proteome Res. 2017 Sep 1;16(9):3298-3309. doi: 10.1021/acs.jproteome.7b00288. Epub 2017 Aug 11.

PMID:
28730805
7.

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

Timmins-Schiffman E, May DH, Mikan M, Riffle M, Frazar C, Harvey HR, Noble WS, Nunn BL.

ISME J. 2017 Feb;11(2):309-314. doi: 10.1038/ismej.2016.132. Epub 2016 Nov 8. No abstract available.

8.

An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.

May DH, Timmins-Schiffman E, Mikan MP, Harvey HR, Borenstein E, Nunn BL, Noble WS.

J Proteome Res. 2016 Aug 5;15(8):2697-705. doi: 10.1021/acs.jproteome.6b00239. Epub 2016 Jul 19.

9.

Proteomics of Colwellia psychrerythraea at subzero temperatures - a life with limited movement, flexible membranes and vital DNA repair.

Nunn BL, Slattery KV, Cameron KA, Timmins-Schiffman E, Junge K.

Environ Microbiol. 2015 Jul;17(7):2319-35. doi: 10.1111/1462-2920.12691. Epub 2015 Feb 5.

PMID:
25471130
10.

Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas.

Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH, Roberts SB.

BMC Genomics. 2014 Nov 3;15:951. doi: 10.1186/1471-2164-15-951.

11.

Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton.

Poulson-Ellestad KL, Jones CM, Roy J, Viant MR, Fernández FM, Kubanek J, Nunn BL.

Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):9009-14. doi: 10.1073/pnas.1402130111. Epub 2014 Jun 2. Erratum in: Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12568.

12.

Diatom proteomics reveals unique acclimation strategies to mitigate Fe limitation.

Nunn BL, Faux JF, Hippmann AA, Maldonado MT, Harvey HR, Goodlett DR, Boyd PW, Strzepek RF.

PLoS One. 2013 Oct 16;8(10):e75653. doi: 10.1371/journal.pone.0075653. eCollection 2013.

13.

Sample preparation and processing for planktonic microbial community proteomics.

Morris RM, Nunn BL.

Methods Enzymol. 2013;531:271-87. doi: 10.1016/B978-0-12-407863-5.00014-9.

PMID:
24060126
14.

Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean.

Mattes TE, Nunn BL, Marshall KT, Proskurowski G, Kelley DS, Kawka OE, Goodlett DR, Hansell DA, Morris RM.

ISME J. 2013 Dec;7(12):2349-60. doi: 10.1038/ismej.2013.113. Epub 2013 Jul 11.

15.

Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster.

Timmins-Schiffman E, Nunn BL, Goodlett DR, Roberts SB.

Conserv Physiol. 2013 May 17;1(1):cot009. doi: 10.1093/conphys/cot009. eCollection 2013.

16.

Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments.

Moore EK, Nunn BL, Goodlett DR, Harvey HR.

Geochim Cosmochim Acta. 2012 Apr 15;83:324-359. Epub 2012 Jan 24.

17.

Acquisition of iron by alkaliphilic bacillus species.

McMillan DG, Velasquez I, Nunn BL, Goodlett DR, Hunter KA, Lamont I, Sander SG, Cook GM.

Appl Environ Microbiol. 2010 Oct;76(20):6955-61. doi: 10.1128/AEM.01393-10. Epub 2010 Aug 27.

18.

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction.

Morris RM, Nunn BL, Frazar C, Goodlett DR, Ting YS, Rocap G.

ISME J. 2010 May;4(5):673-85. doi: 10.1038/ismej.2010.4. Epub 2010 Feb 18.

PMID:
20164862
19.

Deciphering diatom biochemical pathways via whole-cell proteomics.

Nunn BL, Aker JR, Shaffer SA, Tsai S, Strzepek RF, Boyd PW, Freeman TL, Brittnacher M, Malmström L, Goodlett DR.

Aquat Microb Ecol. 2009 Jun 3;55(3):241-253.

20.

Tandem mass spectrometry investigation of ADP-ribosylated kemptide.

Hengel SM, Shaffer SA, Nunn BL, Goodlett DR.

J Am Soc Mass Spectrom. 2009 Mar;20(3):477-83. doi: 10.1016/j.jasms.2008.10.025. Epub 2008 Nov 17.

21.

Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO.

Nunn BL, Shaffer SA, Scherl A, Gallis B, Wu M, Miller SI, Goodlett DR.

Brief Funct Genomic Proteomic. 2006 Jun;5(2):154-68. Review.

PMID:
16798750

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