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Items: 1 to 20 of 110


Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags.

Shen Y, Tolić N, Hixson KK, Purvine SO, Pasa-Tolić L, Qian WJ, Adkins JN, Moore RJ, Smith RD.

Anal Chem. 2008 Mar 15;80(6):1871-82. doi: 10.1021/ac702328x. Epub 2008 Feb 14.


De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins.

Shen Y, Tolić N, Hixson KK, Purvine SO, Anderson GA, Smith RD.

Anal Chem. 2008 Oct 15;80(20):7742-54. doi: 10.1021/ac801123p. Epub 2008 Sep 11.


Large Scale Mass Spectrometry-based Identifications of Enzyme-mediated Protein Methylation Are Subject to High False Discovery Rates.

Hart-Smith G, Yagoub D, Tay AP, Pickford R, Wilkins MR.

Mol Cell Proteomics. 2016 Mar;15(3):989-1006. doi: 10.1074/mcp.M115.055384. Epub 2015 Dec 23.


Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation.

Helsens K, Van Damme P, Degroeve S, Martens L, Arnesen T, Vandekerckhove J, Gevaert K.

J Proteome Res. 2011 Aug 5;10(8):3578-89. doi: 10.1021/pr2002325. Epub 2011 Jun 20.


Analysis of the acidic proteome with negative electron-transfer dissociation mass spectrometry.

McAlister GC, Russell JD, Rumachik NG, Hebert AS, Syka JE, Geer LY, Westphall MS, Pagliarini DJ, Coon JJ.

Anal Chem. 2012 Mar 20;84(6):2875-82. doi: 10.1021/ac203430u. Epub 2012 Mar 1.


False discovery rates in spectral identification.

Jeong K, Kim S, Bandeira N.

BMC Bioinformatics. 2012;13 Suppl 16:S2. doi: 10.1186/1471-2105-13-S16-S2. Epub 2012 Nov 5.


Transferred subgroup false discovery rate for rare post-translational modifications detected by mass spectrometry.

Fu Y, Qian X.

Mol Cell Proteomics. 2014 May;13(5):1359-68. doi: 10.1074/mcp.O113.030189. Epub 2013 Nov 7.


Analysis of the resolution limitations of peptide identification algorithms.

Colaert N, Degroeve S, Helsens K, Martens L.

J Proteome Res. 2011 Dec 2;10(12):5555-61. doi: 10.1021/pr200913a. Epub 2011 Oct 26.


Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome.

Qian WJ, Liu T, Monroe ME, Strittmatter EF, Jacobs JM, Kangas LJ, Petritis K, Camp DG 2nd, Smith RD.

J Proteome Res. 2005 Jan-Feb;4(1):53-62.


Discovering mercury protein modifications in whole proteomes using natural isotope distributions observed in liquid chromatography-tandem mass spectrometry.

Polacco BJ, Purvine SO, Zink EM, Lavoie SP, Lipton MS, Summers AO, Miller SM.

Mol Cell Proteomics. 2011 Aug;10(8):M110.004853. doi: 10.1074/mcp.M110.004853. Epub 2011 Apr 30.


Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.

Jones AR, Siepen JA, Hubbard SJ, Paton NW.

Proteomics. 2009 Mar;9(5):1220-9. doi: 10.1002/pmic.200800473.


Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching.

Merkley ED, Anderson BJ, Park J, Belchik SM, Shi L, Monroe ME, Smith RD, Lipton MS.

J Proteome Res. 2012 Dec 7;11(12):6147-58. doi: 10.1021/pr3007914. Epub 2012 Nov 2.


Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: the human mammary epithelial cell proteome.

Liu T, Qian WJ, Chen WN, Jacobs JM, Moore RJ, Anderson DJ, Gritsenko MA, Monroe ME, Thrall BD, Camp DG 2nd, Smith RD.

Proteomics. 2005 Apr;5(5):1263-73.


Rapid identification of an antibody DNA construct rearrangement sequence variant by mass spectrometry.

Scott RA, Rogers R, Balland A, Brady LJ.

MAbs. 2014;6(6):1453-63. doi: 10.4161/mabs.36222.


The spectral networks paradigm in high throughput mass spectrometry.

Guthals A, Watrous JD, Dorrestein PC, Bandeira N.

Mol Biosyst. 2012 Oct;8(10):2535-44. doi: 10.1039/c2mb25085c. Review.


Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry.

Strittmatter EF, Ferguson PL, Tang K, Smith RD.

J Am Soc Mass Spectrom. 2003 Sep;14(9):980-91.


Global analysis of the cortical neuron proteome.

Yu LR, Conrads TP, Uo T, Kinoshita Y, Morrison RS, Lucas DA, Chan KC, Blonder J, Issaq HJ, Veenstra TD.

Mol Cell Proteomics. 2004 Sep;3(9):896-907. Epub 2004 Jun 30.


A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.

Savitski MM, Wilhelm M, Hahne H, Kuster B, Bantscheff M.

Mol Cell Proteomics. 2015 Sep;14(9):2394-404. doi: 10.1074/mcp.M114.046995. Epub 2015 May 17.


DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data.

Fu Y, Xiu LY, Jia W, Ye D, Sun RX, Qian XH, He SM.

Mol Cell Proteomics. 2011 May;10(5):M110.000455. doi: 10.1074/mcp.M110.000455. Epub 2011 Feb 14.

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