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Ruggles KV, Krug K, Wang X, et al. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics. 2017;16(6):959-981doi: 10.1074/mcp.MR117.000024.
Ruggles, K. V., Krug, K., Wang, X., Clauser, K. R., Wang, J., Payne, S. H., Fenyö, D., Zhang, B., & Mani, D. R. (2017). Methods, Tools and Current Perspectives in Proteogenomics. Molecular & cellular proteomics : MCP, 16(6), 959-981. https://doi.org/10.1074/mcp.MR117.000024
Ruggles, Kelly V, et al. "Methods, Tools and Current Perspectives in Proteogenomics." Molecular & cellular proteomics : MCP vol. 16,6 (2017): 959-981. doi: https://doi.org/10.1074/mcp.MR117.000024
Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29. PMID: 28456751; PMCID: PMC5461547.
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Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29.

Methods, Tools and Current Perspectives in Proteogenomics.

Molecular & cellular proteomics : MCP

Kelly V Ruggles, Karsten Krug, Xiaojing Wang, Karl R Clauser, Jing Wang, Samuel H Payne, David Fenyö, Bing Zhang, D R Mani

Affiliations

  1. From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016.
  2. §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
  3. ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.
  4. ?Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030.
  5. **Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354.
  6. ‡‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016; [email protected] [email protected] [email protected].
  7. §§Institute for Systems Genetics, New York University School of Medicine, New York, New York 10016.
  8. ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030; [email protected] [email protected] [email protected].
  9. §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142; [email protected] [email protected] [email protected].

PMID: 28456751 PMCID: PMC5461547 DOI: 10.1074/mcp.MR117.000024

Abstract

With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics,

© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

References

  1. Sci Rep. 2016 Aug 26;6:31730 - PubMed
  2. J Proteome Res. 2013 Jan 4;12(1):179-86 - PubMed
  3. BMC Bioinformatics. 2009 Nov 12;10:375 - PubMed
  4. Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3932-7 - PubMed
  5. Nat Microbiol. 2016 Jul;1(7):16068 - PubMed
  6. J Proteome Res. 2016 Mar 4;15(3):795-9 - PubMed
  7. Genome Biol. 2013;14(10):R110 - PubMed
  8. Anim Genet. 2010 Dec;41 Suppl 2:121-30 - PubMed
  9. Bioinformatics. 2016 Mar 1;32(5):767-9 - PubMed
  10. BMC Genomics. 2012 Apr 05;13:131 - PubMed
  11. Nat Protoc. 2007;2(10):2366-82 - PubMed
  12. Cell. 2011 Mar 18;144(6):844-9 - PubMed
  13. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 - PubMed
  14. Proteomics. 2014 Dec;14(23-24):2699-708 - PubMed
  15. J Proteome Res. 2013 Jun 7;12(6):2846-57 - PubMed
  16. Nature. 2010 Aug 12;466(7308):835-40 - PubMed
  17. Mol Cell Proteomics. 2015 Nov;14(11):2947-60 - PubMed
  18. Cell Syst. 2016 Oct 26;3(4):361-373.e6 - PubMed
  19. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W77-83 - PubMed
  20. Proteomics. 2004 Jan;4(1):59-77 - PubMed
  21. J Exp Med. 2013 Feb 11;210(2):389-99 - PubMed
  22. J Proteome Res. 2014 Jan 3;13(1):21-8 - PubMed
  23. Nucleic Acids Res. 2017 Jan 4;45(D1):D635-D642 - PubMed
  24. Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):521-45 - PubMed
  25. Nat Methods. 2014 Nov;11(11):1107-13 - PubMed
  26. Cell. 2016 Jul 28;166(3):755-65 - PubMed
  27. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W115-21 - PubMed
  28. Cell. 2012 May 11;149(4):740-52 - PubMed
  29. Annu Rev Anal Chem (Palo Alto Calif). 2015 ;8:61-80 - PubMed
  30. Bioinformatics. 2012 Feb 15;28(4):573-80 - PubMed
  31. Nat Biotechnol. 2011 May;29(5):391-3 - PubMed
  32. Mol Cell. 2015 Jan 22;57(2):349-60 - PubMed
  33. Mol Cell Proteomics. 2010 Apr;9(4):623-34 - PubMed
  34. Annu Rev Biochem. 2007;76:1-22 - PubMed
  35. J Hum Genet. 2007;52(11):871-80 - PubMed
  36. J Proteome Res. 2015 Sep 4;14(9):3729-37 - PubMed
  37. Mol Syst Biol. 2008;4:218 - PubMed
  38. Bioinformatics. 2010 Jun 15;26(12):i399-406 - PubMed
  39. Genome Res. 2008 Oct;18(10):1660-9 - PubMed
  40. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W423-6 - PubMed
  41. J Mass Spectrom. 2005 Apr;40(4):430-43 - PubMed
  42. Mol Syst Biol. 2013;9:637 - PubMed
  43. Bioinformatics. 2009 Jan 1;25(1):75-82 - PubMed
  44. Clin Proteomics. 2011 Jul 08;8(1):11 - PubMed
  45. Genome Res. 2007 Sep;17(9):1362-77 - PubMed
  46. Nat Rev Genet. 2012 Mar 13;13(4):227-32 - PubMed
  47. Annu Rev Genet. 2012;46:651-75 - PubMed
  48. J Proteomics Bioinform. 2015;8(9):204-211 - PubMed
  49. Sci Signal. 2013 Sep 24;6(294):ra84 - PubMed
  50. Science. 2015 Feb 6;347(6222):664-7 - PubMed
  51. Bioinformatics. 2011 Feb 1;27(3):431-2 - PubMed
  52. Proc Natl Acad Sci U S A. 2016 May 24;113(21):5970-5 - PubMed
  53. J Proteome Res. 2015 May 1;14(5):2255-66 - PubMed
  54. Nat Genet. 2009 Feb;41(2):166-7 - PubMed
  55. Nat Commun. 2016 Jan 04;7:10259 - PubMed
  56. Nature. 2013 Sep 26;501(7468):506-11 - PubMed
  57. Bioinformatics. 2014 Dec 1;30(23):3410-1 - PubMed
  58. Nature. 2016 Sep 14;537(7620):347-55 - PubMed
  59. J Proteome Res. 2016 Mar 4;15(3):755-65 - PubMed
  60. Nat Methods. 2010 Mar;7(3 Suppl):S56-68 - PubMed
  61. Cell Syst. 2015 Oct 28;1(4):302-305 - PubMed
  62. BMC Syst Biol. 2012 Nov 10;6:139 - PubMed
  63. Proc Natl Acad Sci U S A. 1941 Nov 15;27(11):499-506 - PubMed
  64. Nature. 2014 Sep 18;513(7518):382-7 - PubMed
  65. J Proteome Res. 2015 Sep 4;14(9):3555-67 - PubMed
  66. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):21034-8 - PubMed
  67. New Phytol. 2011 Feb;189(3):883-91 - PubMed
  68. Mol Cell Proteomics. 2015 Nov;14(11):3087-93 - PubMed
  69. Anal Chem. 1999 Jul 15;71(14):2871-82 - PubMed
  70. Cell. 2015 Sep 24;163(1):202-17 - PubMed
  71. Mol Cell Proteomics. 2014 Dec;13(12):3698-708 - PubMed
  72. Nucleic Acids Res. 2001 Jan 1;29(1):308-11 - PubMed
  73. J Proteome Res. 2004 Nov-Dec;3(6):1234-42 - PubMed
  74. Genome Biol. 2005;6(1):R9 - PubMed
  75. Cell. 2007 Aug 10;130(3):395-8 - PubMed
  76. Bioinformatics. 2016 Oct 1;32(19):3041-3 - PubMed
  77. BMC Genomics. 2014 Aug 22;15:703 - PubMed
  78. Cell. 2001 Feb 9;104(3):333-9 - PubMed
  79. Nat Genet. 1998 Sep;20(1):46-50 - PubMed
  80. OMICS. 2005 Winter;9(4):301-33 - PubMed
  81. J Proteome Res. 2016 Jul 1;15(7):2309-20 - PubMed
  82. Nature. 2009 Nov 5;462(7269):108-12 - PubMed
  83. BMC Genomics. 2009 Aug 07;10:365 - PubMed
  84. Trends Pharmacol Sci. 2014 Sep;35(9):450-60 - PubMed
  85. Proteomics. 2014 Dec;14(23-24):2676-87 - PubMed
  86. Mol Cell Proteomics. 2013 Nov;12(11):3420-30 - PubMed
  87. PLoS Comput Biol. 2012;8(12):e1002822 - PubMed
  88. Mol Cell Proteomics. 2016 Nov;15(11):3501-3512 - PubMed
  89. Cancer Res. 2014 Jan 1;74(1):387-97 - PubMed
  90. Nat Genet. 2007 Nov;39(11):1369-75 - PubMed
  91. Protein Pept Lett. 2015;22(11):983-91 - PubMed
  92. Science. 2015 Mar 6;347(6226):1066-7 - PubMed
  93. Front Microbiol. 2016 Apr 05;7:427 - PubMed
  94. Nucleic Acids Res. 2009 Mar;37(4):1297-307 - PubMed
  95. Genome Res. 2010 Jun;20(6):837-46 - PubMed
  96. Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72 - PubMed
  97. Nature. 2008 Sep 4;455(7209):58-63 - PubMed
  98. Mol Cell Proteomics. 2016 Mar;15(3):1164-75 - PubMed
  99. Bioinformatics. 2008 Aug 15;24(16):i14-20 - PubMed
  100. J Biol Chem. 2009 Jan 30;284(5):3273-84 - PubMed
  101. Bioinformatics. 2010 Jun 15;26(12):i237-45 - PubMed
  102. Genome Biol. 2006;7(4):R35 - PubMed
  103. Mol Cell Proteomics. 2013 Jul;12(7):1900-11 - PubMed
  104. Nat Biotechnol. 2006 May;24(5):537-44 - PubMed
  105. Stand Genomic Sci. 2015 Jul 25;10:45 - PubMed
  106. Nature. 2008 Sep 4;455(7209):64-71 - PubMed
  107. Mol Cell Proteomics. 2012 Oct;11(10):1084-96 - PubMed
  108. J Proteome Res. 2014 Jan 3;13(1):84-98 - PubMed
  109. Science. 2008 May 16;320(5878):938-41 - PubMed
  110. Stat Appl Genet Mol Biol. 2004;3:Article3 - PubMed
  111. J Proteome Res. 2008 May;7(5):1873-83 - PubMed
  112. Mol Syst Biol. 2012 Jan 17;8:565 - PubMed
  113. Nature. 2011 Dec 21;481(7381):371-5 - PubMed
  114. J Clin Invest. 2009 Jun;119(6):1727-40 - PubMed
  115. Nat Biotechnol. 2012 Mar 25;30(5):447-52 - PubMed
  116. Bioinformatics. 2013 Dec 15;29(24):3235-7 - PubMed
  117. PLoS One. 2012;7(12):e50246 - PubMed
  118. J Proteome Res. 2016 Mar 4;15(3):721-31 - PubMed
  119. Sci Rep. 2013 Oct 02;3:2651 - PubMed
  120. Trends Genet. 2008 Aug;24(8):408-15 - PubMed
  121. Methods Mol Biol. 2010;604:55-71 - PubMed
  122. Genome Biol. 2003;4(5):P3 - PubMed
  123. Proteomics. 2014 Dec;14(23-24):2731-41 - PubMed
  124. Cell. 2004 Jan 23;116(2):281-97 - PubMed
  125. Nature. 2012 Mar 28;483(7391):570-5 - PubMed
  126. Cell Rep. 2013 Aug 15;4(3):609-20 - PubMed
  127. Cell. 1998 Aug 21;94(4):411-4 - PubMed
  128. Bioinformatics. 2015 Jun 15;31(12):i197-205 - PubMed
  129. BMC Bioinformatics. 2016 Jun 17;17(1):244 - PubMed
  130. Nat Biotechnol. 2011 Jan;29(1):24-6 - PubMed
  131. Environ Microbiol. 2004 Sep;6(9):911-20 - PubMed
  132. Nat Methods. 2013 Jul;10(7):597-8 - PubMed
  133. J Proteome Res. 2014 Jun 6;13(6):2715-23 - PubMed
  134. BMC Genomics. 2015 Dec 01;16:1022 - PubMed
  135. Cell. 2016 Apr 21;165(3):535-50 - PubMed
  136. Nat Methods. 2014 Dec;11(12):1253-60 - PubMed
  137. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:52-9 - PubMed
  138. Mol Cell Proteomics. 2012 Mar;11(3):O111.013698 - PubMed
  139. Genome Res. 2009 Jan;19(1):128-35 - PubMed
  140. Proc Natl Acad Sci U S A. 2013 Mar 12;110(11):4245-50 - PubMed
  141. PLoS Biol. 2011 Sep;9(9):e1001144 - PubMed
  142. Nat Biotechnol. 2007 Jun;25(6):651-5 - PubMed
  143. Eur Urol. 2016 May;69(5):942-52 - PubMed
  144. Genome Res. 2007 Feb;17(2):231-9 - PubMed
  145. Genet Med. 2006 Jul;8(7):395-400 - PubMed
  146. Cancer Res. 2016 Aug 1;76(15):4316-9 - PubMed
  147. Am J Pathol. 2014 May;184(5):1280-6 - PubMed
  148. J Proteomics. 2010 Oct 10;73(11):2124-35 - PubMed
  149. Nucleic Acids Res. 2011 Jan;39(Database issue):D261-7 - PubMed
  150. PLoS Genet. 2011 Jun;7(6):e1001393 - PubMed
  151. Cancer Discov. 2012 May;2(5):401-4 - PubMed
  152. Philos Trans R Soc Lond B Biol Sci. 2013 May 06;368(1620):20120362 - PubMed
  153. Nature. 2016 May 25;534(7605):55-62 - PubMed
  154. Sci Rep. 2014 Mar 21;4:4411 - PubMed
  155. J Control Release. 2015 Jan 10;197:190-8 - PubMed
  156. BMC Genomics. 2005 Sep 19;6:128 - PubMed
  157. Genome Biol. 2014 Jun 30;15(6):R86 - PubMed
  158. Nature. 2012 Mar 28;483(7391):603-7 - PubMed
  159. Science. 2015 Mar 6;347(6226):1259038 - PubMed
  160. Anal Chem. 1995 Sep 15;67(18):3202-10 - PubMed
  161. Infect Immun. 2001 Sep;69(9):5905-7 - PubMed
  162. Bioinformatics. 2008 Sep 15;24(18):2112-4 - PubMed
  163. Mass Spectrom Rev. 2015 Dec 15;:null - PubMed
  164. Mol Biosyst. 2011 Feb;7(2):284-91 - PubMed
  165. Mol Cell Proteomics. 2017 Jan;16(1):121-134 - PubMed
  166. Cell. 2011 Mar 18;144(6):986-98 - PubMed
  167. Bioinformatics. 2009 Apr 15;25(8):1004-11 - PubMed
  168. Bioinformatics. 2015 Jun 15;31(12):i106-15 - PubMed
  169. Proteomics. 2015 Oct;15(20):3409-17 - PubMed
  170. Proteomics. 2001 May;1(5):651-67 - PubMed
  171. Genome Biol. 2003;4(4):R28 - PubMed
  172. J Proteome Res. 2017 Jan 6;16(1):45-54 - PubMed
  173. J Proteome Res. 2016 Mar 4;15(3):983-90 - PubMed
  174. Bioinformatics. 2015 Jun 15;31(12):2056-8 - PubMed
  175. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 - PubMed
  176. Proteomics. 2016 Sep;16(18):2495-501 - PubMed
  177. Nat Methods. 2014 Nov;11(11):1114-25 - PubMed
  178. Nat Methods. 2014 Mar;11(3):333-7 - PubMed
  179. BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S10 - PubMed
  180. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14704-8 - PubMed
  181. Mol Cell Proteomics. 2016 Mar;15(3):1060-71 - PubMed
  182. Mass Spectrom Rev. 2015 Jan-Feb;34(1):43-63 - PubMed
  183. Cell. 2014 Aug 14;158(4):929-44 - PubMed
  184. BMC Bioinformatics. 2011 Apr 22;12:115 - PubMed
  185. Biometrics. 2016 Jun;72 (2):575-83 - PubMed
  186. BMC Bioinformatics. 2016 Jan 20;17 Suppl 2:15 - PubMed
  187. BMC Syst Biol. 2008 Nov 28;2:104 - PubMed
  188. Nucleic Acids Res. 2015 Jan;43(Database issue):D512-20 - PubMed
  189. Nat Microbiol. 2016 Apr 11;1:16048 - PubMed
  190. Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12 - PubMed
  191. IEEE Trans Vis Comput Graph. 2008 Nov-Dec;14(6):1253-60 - PubMed
  192. Nat Rev Genet. 2016 Oct;17 (10 ):615-29 - PubMed
  193. Nat Methods. 2015 Jun;12(6):531-3 - PubMed
  194. Genome Biol. 2008;9(7):R116 - PubMed
  195. Electrophoresis. 1997 Aug;18(8):1314-34 - PubMed
  196. Science. 2011 Sep 16;333(6049):1633-7 - PubMed
  197. Annu Rev Biochem. 2012;81:379-405 - PubMed

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