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Items: 20

1.

Stable isotope dimethyl labelling for quantitative proteomics and beyond.

Hsu JL, Chen SH.

Philos Trans A Math Phys Eng Sci. 2016 Oct 28;374(2079). pii: 20150364. doi: 10.1098/rsta.2015.0364. Review.

PMID:
27644970
2.

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.

3.

DeMix-Q: Quantification-Centered Data Processing Workflow.

Zhang B, Käll L, Zubarev RA.

Mol Cell Proteomics. 2016 Apr;15(4):1467-78. doi: 10.1074/mcp.O115.055475. Epub 2016 Jan 4.

4.

Genetic basis of haloperidol resistance in Saccharomyces cerevisiae is complex and dose dependent.

Wang X, Kruglyak L.

PLoS Genet. 2014 Dec 18;10(12):e1004894. doi: 10.1371/journal.pgen.1004894. eCollection 2014 Dec.

5.

mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets.

Bouyssié D, Dubois M, Nasso S, Gonzalez de Peredo A, Burlet-Schiltz O, Aebersold R, Monsarrat B.

Mol Cell Proteomics. 2015 Mar;14(3):771-81. doi: 10.1074/mcp.O114.039115. Epub 2014 Dec 11.

6.

Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms.

Riley BE, Gardai SJ, Emig-Agius D, Bessarabova M, Ivliev AE, Schüle B, Alexander J, Wallace W, Halliday GM, Langston JW, Braxton S, Yednock T, Shaler T, Johnston JA.

PLoS One. 2014 Aug 29;9(8):e102909. doi: 10.1371/journal.pone.0102909. eCollection 2014. Erratum in: PLoS One. 2014;9(12):e115081. Schüle, Birgit [corrected to Schüle, Birgitt].

7.

Stoichiometry of site-specific lysine acetylation in an entire proteome.

Baeza J, Dowell JA, Smallegan MJ, Fan J, Amador-Noguez D, Khan Z, Denu JM.

J Biol Chem. 2014 Aug 1;289(31):21326-38. doi: 10.1074/jbc.M114.581843. Epub 2014 Jun 10.

8.

Genetics of single-cell protein abundance variation in large yeast populations.

Albert FW, Treusch S, Shockley AH, Bloom JS, Kruglyak L.

Nature. 2014 Feb 27;506(7489):494-7. doi: 10.1038/nature12904. Epub 2014 Jan 8.

9.

A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide-spectrum matches in shotgun proteomics experiments.

Ruse CI, Peacock S, Ghiban C, Rivera K, Pappin DJ, Leopold P.

Proteomics. 2013 Aug;13(16):2386-97. doi: 10.1002/pmic.201300022. Epub 2013 Jul 11.

10.

An adaptive alignment algorithm for quality-controlled label-free LC-MS.

Sandin M, Ali A, Hansson K, Månsson O, Andreasson E, Resjö S, Levander F.

Mol Cell Proteomics. 2013 May;12(5):1407-20. doi: 10.1074/mcp.O112.021907. Epub 2013 Jan 9.

11.

Comprehensive analysis of LC/MS data using pseudocolor plots.

Crutchfield CA, Olson MT, Gourgari E, Nesterova M, Stratakis CA, Yergey AL.

J Am Soc Mass Spectrom. 2013 Feb;24(2):230-7. doi: 10.1007/s13361-012-0524-6. Epub 2013 Jan 3.

12.

Tools for label-free peptide quantification.

Nahnsen S, Bielow C, Reinert K, Kohlbacher O.

Mol Cell Proteomics. 2013 Mar;12(3):549-56. doi: 10.1074/mcp.R112.025163. Epub 2012 Dec 17. Review.

13.

Proteomic classification of acute leukemias by alignment-based quantitation of LC-MS/MS data sets.

Foss EJ, Radulovic D, Stirewalt DL, Radich J, Sala-Torra O, Pogosova-Agadjanyan EL, Hengel SM, Loeb KR, Deeg HJ, Meshinchi S, Goodlett DR, Bedalov A.

J Proteome Res. 2012 Oct 5;11(10):5005-10. doi: 10.1021/pr300567r. Epub 2012 Sep 11.

14.

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.

Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L.

Mol Syst Biol. 2012;8:602. doi: 10.1038/msb.2012.34.

15.

Current challenges in software solutions for mass spectrometry-based quantitative proteomics.

Cappadona S, Baker PR, Cutillas PR, Heck AJ, van Breukelen B.

Amino Acids. 2012 Sep;43(3):1087-108. doi: 10.1007/s00726-012-1289-8. Epub 2012 Jul 22. Review.

16.

Global secretome analysis identifies novel mediators of bone metastasis.

Blanco MA, LeRoy G, Khan Z, Alečković M, Zee BM, Garcia BA, Kang Y.

Cell Res. 2012 Sep;22(9):1339-55. doi: 10.1038/cr.2012.89. Epub 2012 Jun 12.

17.

BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection.

Lee SH, Kalejta RF, Kerry J, Semmes OJ, O'Connor CM, Khan Z, Garcia BA, Shenk T, Murphy E.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9575-80. doi: 10.1073/pnas.1207496109. Epub 2012 May 29.

18.

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.

Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S.

Genome Biol. 2011 Dec 19;12(12):R122. doi: 10.1186/gb-2011-12-12-r122.

19.

Protein quantitation using mass spectrometry.

Zhang G, Ueberheide BM, Waldemarson S, Myung S, Molloy K, Eriksson J, Chait BT, Neubert TA, Fenyö D.

Methods Mol Biol. 2010;673:211-22. doi: 10.1007/978-1-60761-842-3_13.

20.

Identification of quantitative trait loci underlying proteome variation in human lymphoblastoid cells.

Garge N, Pan H, Rowland MD, Cargile BJ, Zhang X, Cooley PC, Page GP, Bunger MK.

Mol Cell Proteomics. 2010 Jul;9(7):1383-99. doi: 10.1074/mcp.M900378-MCP200. Epub 2010 Feb 23.

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