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Items: 17

1.

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.

2.

Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA).

Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M.

Mol Cell Proteomics. 2015 Feb;14(2):430-40. doi: 10.1074/mcp.M114.044321. Epub 2014 Dec 3.

3.

Targeted quantitation of proteins by mass spectrometry.

Liebler DC, Zimmerman LJ.

Biochemistry. 2013 Jun 4;52(22):3797-806. doi: 10.1021/bi400110b. Epub 2013 Mar 27. Review.

4.

Optimal precursor ion selection for LC-MALDI MS/MS.

Zerck A, Nordhoff E, Lehrach H, Reinert K.

BMC Bioinformatics. 2013 Feb 18;14:56. doi: 10.1186/1471-2105-14-56.

5.

Learning from decoys to improve the sensitivity and specificity of proteomics database search results.

Yadav AK, Kumar D, Dash D.

PLoS One. 2012;7(11):e50651. doi: 10.1371/journal.pone.0050651. Epub 2012 Nov 26.

6.

Computational approaches to protein inference in shotgun proteomics.

Li YF, Radivojac P.

BMC Bioinformatics. 2012;13 Suppl 16:S4. doi: 10.1186/1471-2105-13-S16-S4. Epub 2012 Nov 5. Review.

7.

A critical assessment of feature selection methods for biomarker discovery in clinical proteomics.

Christin C, Hoefsloot HC, Smilde AK, Hoekman B, Suits F, Bischoff R, Horvatovich P.

Mol Cell Proteomics. 2013 Jan;12(1):263-76. doi: 10.1074/mcp.M112.022566. Epub 2012 Oct 31.

8.

The development of selected reaction monitoring methods for targeted proteomics via empirical refinement.

Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ.

Proteomics. 2012 Apr;12(8):1134-41. doi: 10.1002/pmic.201200042. Review.

9.

Computational and statistical analysis of protein mass spectrometry data.

Noble WS, MacCoss MJ.

PLoS Comput Biol. 2012 Jan;8(1):e1002296. doi: 10.1371/journal.pcbi.1002296. Epub 2012 Jan 26. Review.

10.
11.

The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics.

Li YF, Arnold RJ, Tang H, Radivojac P.

J Proteome Res. 2010 Dec 3;9(12):6288-97. doi: 10.1021/pr1005586. Epub 2010 Nov 10.

12.

Assigning statistical significance to proteotypic peptides via database searches.

Alves G, Ogurtsov AY, Yu YK.

J Proteomics. 2011 Feb 1;74(2):199-211. doi: 10.1016/j.jprot.2010.10.005. Epub 2010 Nov 3.

13.

Machine learning based prediction for peptide drift times in ion mobility spectrometry.

Shah AR, Agarwal K, Baker ES, Singhal M, Mayampurath AM, Ibrahim YM, Kangas LJ, Monroe ME, Zhao R, Belov ME, Anderson GA, Smith RD.

Bioinformatics. 2010 Jul 1;26(13):1601-7. doi: 10.1093/bioinformatics/btq245. Epub 2010 May 21.

14.

Synthetic peptide arrays for pathway-level protein monitoring by liquid chromatography-tandem mass spectrometry.

Hewel JA, Liu J, Onishi K, Fong V, Chandran S, Olsen JB, Pogoutse O, Schutkowski M, Wenschuh H, Winkler DF, Eckler L, Zandstra PW, Emili A.

Mol Cell Proteomics. 2010 Nov;9(11):2460-73. doi: 10.1074/mcp.M900456-MCP200. Epub 2010 May 13.

15.

Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction.

Mujezinovic N, Schneider G, Wildpaner M, Mechtler K, Eisenhaber F.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S13. doi: 10.1186/1471-2164-11-S1-S13.

16.

Proteomics data repositories.

Riffle M, Eng JK.

Proteomics. 2009 Oct;9(20):4653-63. doi: 10.1002/pmic.200900216. Review.

17.

Prediction of high-responding peptides for targeted protein assays by mass spectrometry.

Fusaro VA, Mani DR, Mesirov JP, Carr SA.

Nat Biotechnol. 2009 Feb;27(2):190-8. doi: 10.1038/nbt.1524. Epub 2009 Jan 25.

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