Display options
Cite
van Wijk KJ, Leppert T, Sun Q, et al. The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. Plant Cell. 2021;33(11):3421-3453doi: 10.1093/plcell/koab211.
van Wijk, K. J., Leppert, T., Sun, Q., Boguraev, S. S., Sun, Z., Mendoza, L., & Deutsch, E. W. (2021). The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. The Plant cell, 33(11), 3421-3453. https://doi.org/10.1093/plcell/koab211
van Wijk, Klaas J, et al. "The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource." The Plant cell vol. 33,11 (2021): 3421-3453. doi: https://doi.org/10.1093/plcell/koab211
van Wijk KJ, Leppert T, Sun Q, Boguraev SS, Sun Z, Mendoza L, Deutsch EW. The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. Plant Cell. 2021 Nov 04;33(11):3421-3453. doi: 10.1093/plcell/koab211. PMID: 34411258; PMCID: PMC8566204.
Copy Download .nbib Format: NLM
Share it on

Plant Cell. 2021 Nov 04;33(11):3421-3453. doi: 10.1093/plcell/koab211.

The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource.

The Plant cell

Klaas J van Wijk, Tami Leppert, Qi Sun, Sascha S Boguraev, Zhi Sun, Luis Mendoza, Eric W Deutsch

Affiliations

  1. Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA.
  2. Institute for Systems Biology (ISB), Seattle, Washington 98109, USA.
  3. Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, USA.

PMID: 34411258 PMCID: PMC8566204 DOI: 10.1093/plcell/koab211

Abstract

We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.

© American Society of Plant Biologists 2021. All rights reserved. For permissions, please email: [email protected].

References

  1. Genome Biol. 2006;7(11):R106 - PubMed
  2. Proteomics. 2003 Jul;3(7):1374-6 - PubMed
  3. Nat Protoc. 2011 Jul 14;6(8):1130-41 - PubMed
  4. Proteomics. 2015 Jul;15(14):2447-57 - PubMed
  5. Plant Physiol. 2011 Jan;155(1):259-70 - PubMed
  6. Nat Chem Biol. 2018 Jul;14(7):671-679 - PubMed
  7. Nat Methods. 2017 May;14(5):513-520 - PubMed
  8. J Biol Chem. 2002 Mar 8;277(10):8354-65 - PubMed
  9. Plant Cell. 2006 Mar;18(3):545-59 - PubMed
  10. Annu Rev Plant Biol. 2019 Apr 29;70:119-151 - PubMed
  11. J Proteome Res. 2016 Nov 4;15(11):3998-4019 - PubMed
  12. Mol Syst Biol. 2005;1:2005.0017 - PubMed
  13. Proteomics. 2018 May;18(10):e1700038 - PubMed
  14. Front Plant Sci. 2017 May 29;8:894 - PubMed
  15. Front Plant Sci. 2016 Aug 30;7:1314 - PubMed
  16. Nature. 2000 Dec 14;408(6814):796-815 - PubMed
  17. Expert Rev Proteomics. 2020 Jul - Aug;17(7-8):595-607 - PubMed
  18. Proteomics. 2017 Nov;17(21): - PubMed
  19. Nat Commun. 2015 Jul 17;6:7640 - PubMed
  20. Front Plant Sci. 2019 Jul 30;10:974 - PubMed
  21. J Proteome Res. 2016 Oct 7;15(10):3896-3903 - PubMed
  22. Proteomics Clin Appl. 2015 Aug;9(7-8):745-54 - PubMed
  23. Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028 - PubMed
  24. J Proteome Res. 2009 Sep;8(9):4172 - PubMed
  25. Nat Biotechnol. 2012 Oct;30(10):918-20 - PubMed
  26. Methods Mol Biol. 2015;1306:207-16 - PubMed
  27. J Proteomics. 2013 Nov 20;93:5-19 - PubMed
  28. Plant J. 2020 Jan;101(2):420-441 - PubMed
  29. Plant Physiol. 2019 Aug;180(4):2034-2048 - PubMed
  30. J Biol Chem. 2001 May 11;276(19):16318-27 - PubMed
  31. Plant Cell. 2000 Mar;12(3):319-41 - PubMed
  32. Nat Plants. 2016 Feb 01;2:15225 - PubMed
  33. Nat Biotechnol. 2014 Mar;32(3):223-6 - PubMed
  34. Front Plant Sci. 2017 Jul 21;8:1292 - PubMed
  35. J Exp Bot. 2015 May;66(10):2935-44 - PubMed
  36. J Exp Bot. 2015 May;66(10):2923-34 - PubMed
  37. Plant J. 2019 Nov;100(3):438-455 - PubMed
  38. BMC Genomics. 2015 Jul 18;16:533 - PubMed
  39. Int J Mol Sci. 2019 Oct 01;20(19): - PubMed
  40. Anal Chem. 2002 Oct 15;74(20):5383-92 - PubMed
  41. Mol Cell Proteomics. 2019 Jul;18(7):1345-1362 - PubMed
  42. PLoS One. 2008 Apr 23;3(4):e1994 - PubMed
  43. J Proteome Res. 2017 Mar 3;16(3):1352-1363 - PubMed
  44. Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106 - PubMed
  45. J Proteome Res. 2019 Mar 1;18(3):826-840 - PubMed
  46. J Proteome Res. 2020 Dec 4;19(12):4735-4746 - PubMed
  47. Plant J. 2017 Jun;90(6):1176-1186 - PubMed
  48. FEBS J. 2008 Apr;275(8):1767-77 - PubMed
  49. Mol Syst Biol. 2017 Oct 23;13(10):949 - PubMed
  50. Mob DNA. 2020 Jul 27;11:28 - PubMed
  51. J Proteome Res. 2016 Nov 4;15(11):3961-3970 - PubMed
  52. Nat Plants. 2019 May;5(5):525-538 - PubMed
  53. Plant Physiol. 2020 Sep;184(1):110-129 - PubMed
  54. Biomolecules. 2015 Apr 14;5(2):378-411 - PubMed
  55. Nat Plants. 2019 Mar;5(3):316-327 - PubMed
  56. Trends Cell Biol. 2010 Apr;20(4):223-32 - PubMed
  57. J Proteome Res. 2020 Jan 3;19(1):537-542 - PubMed
  58. Trends Biochem Sci. 2017 Jun;42(6):407-408 - PubMed
  59. Annu Rev Anal Chem (Palo Alto Calif). 2015;8:61-80 - PubMed
  60. Plant Cell. 2017 Nov;29(11):2687-2710 - PubMed
  61. PLoS One. 2016 May 03;11(5):e0154235 - PubMed
  62. Plant Cell. 2002 Jan;14(1):211-36 - PubMed
  63. J Proteomics. 2017 Oct 3;169:176-188 - PubMed
  64. Annu Rev Anal Chem (Palo Alto Calif). 2018 Jun 12;11(1):49-77 - PubMed
  65. J Proteome Res. 2017 Dec 1;16(12):4288-4298 - PubMed
  66. BMC Genomics. 2007 Jun 12;8:163 - PubMed
  67. Nucleic Acids Res. 2017 Jan 4;45(D1):D1064-D1074 - PubMed
  68. Plant Physiol. 2015 Mar;167(3):972-90 - PubMed
  69. Mol Cell Proteomics. 2014 Jan;13(1):157-67 - PubMed
  70. Genome Res. 2001 May;11(5):703-9 - PubMed
  71. J Proteome Res. 2019 Dec 6;18(12):4098-4107 - PubMed
  72. Plant Physiol. 2004 Jun;135(2):723-34 - PubMed
  73. Trends Plant Sci. 2021 Apr;26(4):375-391 - PubMed
  74. Proteomics. 2015 Mar;15(5-6):1127-41 - PubMed
  75. Nat Biotechnol. 2008 Aug;26(8):864-6 - PubMed
  76. Proteomics. 2012 Sep;12(18):2895-9 - PubMed
  77. EMBO Rep. 2019 Aug;20(8):e47182 - PubMed
  78. Mol Cell Proteomics. 2015 Feb;14(2):399-404 - PubMed
  79. Front Physiol. 2016 Feb 05;7:26 - PubMed
  80. Mass Spectrom Rev. 2018 Nov;37(6):715-737 - PubMed
  81. Plant Physiol. 2015 Nov;169(3):1881-96 - PubMed
  82. Plant Physiol. 2000 Feb;122(2):295-318 - PubMed
  83. BMC Plant Biol. 2018 Sep 12;18(1):192 - PubMed
  84. J Proteome Res. 2019 Dec 6;18(12):4108-4116 - PubMed
  85. J Proteome Res. 2019 Jul 5;18(7):2719-2734 - PubMed
  86. Mol Cell Proteomics. 2011 Sep;10(9):M110.006353 - PubMed
  87. J Proteomics. 2014 Jan 31;97:62-8 - PubMed
  88. Plant Methods. 2015 Jan 16;11(1):2 - PubMed
  89. Front Plant Sci. 2016 Aug 02;7:1107 - PubMed
  90. Curr Opin Plant Biol. 2019 Oct;51:88-95 - PubMed
  91. Plant J. 2019 Aug;99(4):752-762 - PubMed
  92. Mol Cell Proteomics. 2019 Jan;18(1):86-98 - PubMed
  93. Nat Commun. 2017 Jul 13;8(1):72 - PubMed
  94. Plant Cell. 2018 Mar;30(3):525-527 - PubMed
  95. J Exp Bot. 2020 Sep 19;71(18):5323-5332 - PubMed
  96. Database (Oxford). 2013 Mar 12;2013:bat009 - PubMed
  97. Nat Biotechnol. 2015 Jul;33(7):743-9 - PubMed
  98. Science. 2001 Jun 29;292(5526):2482-5 - PubMed
  99. Mol Plant. 2020 Jul 6;13(7):1078-1093 - PubMed
  100. Mol Cell Proteomics. 2014 Aug;13(8):2147-67 - PubMed
  101. J Exp Bot. 2013 Dec;64(17):5371-81 - PubMed
  102. J Biol Chem. 2020 Jan 24;295(4):1036-1046 - PubMed
  103. Plant Physiol. 2020 Mar;182(3):1510-1526 - PubMed
  104. Plant Physiol. 2019 Aug;180(4):1829-1847 - PubMed
  105. Plant J. 2019 Oct;100(2):411-429 - PubMed
  106. DNA Res. 1999 Oct 29;6(5):283-90 - PubMed
  107. Plant J. 2020 Mar;101(5):1040-1056 - PubMed
  108. Mol Cell Proteomics. 2017 Jun;16(6):1064-1080 - PubMed
  109. Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450 - PubMed
  110. Genome Res. 2007 May;17(5):632-40 - PubMed
  111. Proteomics. 2004 Jun;4(6):1534-6 - PubMed
  112. J Proteome Res. 2016 Nov 4;15(11):4091-4100 - PubMed
  113. Annu Rev Genet. 2013;47:335-52 - PubMed
  114. Mol Cell Proteomics. 2011 Dec;10(12):M111.007690 - PubMed
  115. Plant Physiol. 2013 Nov;163(3):1218-29 - PubMed
  116. Plant J. 2017 Feb;89(4):789-804 - PubMed
  117. Nat Plants. 2019 Jan;5(1):106-117 - PubMed
  118. Mitochondrion. 2017 Mar;33:58-71 - PubMed
  119. Photosynth Res. 2020 Jul;145(1):43-54 - PubMed
  120. Proteomics. 2016 Feb;16(4):634-44 - PubMed
  121. J Proteome Res. 2017 Apr 7;16(4):1410-1424 - PubMed
  122. Nucleic Acids Res. 2009 Jan;37(Database issue):D969-74 - PubMed
  123. Electrophoresis. 2018 Jul;39(13):1543-1557 - PubMed
  124. J Biol Chem. 2019 Dec 20;294(51):19683-19708 - PubMed
  125. Science. 2019 Mar 22;363(6433): - PubMed
  126. Plant Physiol. 2001 Dec;127(4):1711-27 - PubMed
  127. Plant Physiol. 2014 May 7;165(3):1171-1187 - PubMed
  128. BMC Bioinformatics. 2017 Jan 17;18(1):37 - PubMed
  129. Anal Chem. 2009 Oct 1;81(19):8015-24 - PubMed
  130. Nucleic Acids Res. 2013 Jan;41(Database issue):D1185-91 - PubMed
  131. Nature. 2020 Mar;579(7799):409-414 - PubMed
  132. Plant J. 2017 Aug;91(3):518-533 - PubMed
  133. J Mol Recognit. 2019 Jan;32(1):e2754 - PubMed
  134. Plant Cell. 2019 Jun;31(6):1308-1327 - PubMed
  135. Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):E7126-E7135 - PubMed
  136. Plant Cell. 2018 Aug;30(8):1695-1709 - PubMed
  137. Methods Mol Biol. 2018;1829:395-406 - PubMed
  138. Curr Plant Biol. 2015 May 1;2:21-24 - PubMed
  139. BMC Genomics. 2020 Mar 30;21(1):260 - PubMed
  140. Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489 - PubMed
  141. Trends Biochem Sci. 2017 Feb;42(2):98-110 - PubMed
  142. Plant Physiol. 2012 Sep;160(1):2-14 - PubMed
  143. J Exp Bot. 2018 Aug 31;69(19):4555-4568 - PubMed
  144. Genome Biol. 2005;6(1):R9 - PubMed
  145. Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10 - PubMed
  146. Mol Plant. 2017 Jan 9;10(1):197-211 - PubMed
  147. J Proteome Res. 2014 Apr 4;13(4):1969-78 - PubMed
  148. Nat Commun. 2019 Sep 9;10(1):3743 - PubMed
  149. Front Plant Sci. 2016 Jul 12;7:1007 - PubMed
  150. Plant Cell. 2015 Oct;27(10):2677-91 - PubMed
  151. Trends Plant Sci. 2018 Dec;23(12):1068-1080 - PubMed
  152. J Proteome Res. 2019 Dec 6;18(12):4262-4272 - PubMed
  153. Plant Physiol. 2015 Nov;169(3):1469-87 - PubMed
  154. Nucleic Acids Res. 2020 Jan 8;48(D1):D1145-D1152 - PubMed
  155. New Phytol. 2019 May;222(3):1420-1433 - PubMed
  156. Plant Cell. 2016 Dec;28(12):3020-3037 - PubMed
  157. Plant Cell. 2020 Mar;32(3):573-594 - PubMed
  158. Proteomics. 2015 Jul;15(14):2458-69 - PubMed
  159. ACS Chem Biol. 2015 Aug 21;10(8):1754-64 - PubMed
  160. Trends Plant Sci. 2000 Oct;5(10):420-5 - PubMed
  161. Mol Syst Biol. 2018 Mar 1;14(3):e7962 - PubMed
  162. Plant Cell. 2014 Jun 3;26(6):2367-2389 - PubMed
  163. Mol Cell Proteomics. 2011 Jan;10(1):R110.000133 - PubMed
  164. Front Plant Sci. 2013 Oct 23;4:411 - PubMed
  165. Sci Data. 2019 Nov 22;6(1):278 - PubMed
  166. Proteomics. 2020 Nov;20(21-22):e1900362 - PubMed
  167. New Phytol. 2016 Feb;209(3):921-44 - PubMed
  168. Plant J. 2015 Aug;83(3):546-54 - PubMed
  169. Mol Cell Proteomics. 2019 Jul;18(7):1285-1306 - PubMed
  170. Curr Opin Plant Biol. 2018 Oct;45(Pt A):143-154 - PubMed
  171. J Proteome Res. 2019 Jun 7;18(6):2585-2600 - PubMed
  172. Front Plant Sci. 2018 Apr 10;9:461 - PubMed

Publication Types