Skip to main content

Proteomic Data Storage and Sharing

  • Protocol
  • First Online:
Proteome Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1549))

Abstract

With the advent of high-throughput genomic and proteomic techniques, there is a massive amount of multidimensional data being generated and has increased several orders of magnitude. But the amount of data that is cataloged in the central repositories and shared publicly with the scientific community does not correlate the same rate at which the data is generated. Here, in this chapter, we discuss various proteomics data repositories that are freely accessible to the researchers for further downstream meta-analysis.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Mathivanan S (2014) Integrated bioinformatics analysis of the publicly available protein data shows evidence for 96% of the human proteome. J Proteomics Bioinform 07:041–049. doi:10.4172/jpb.1000301

    Article  Google Scholar 

  2. Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A (2014) A draft map of the human proteome. Nature 509(7502):575–581. doi:10.1038/nature13302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B (2014) Mass-spectrometry-based draft of the human proteome. Nature 509(7502):582–587. doi:10.1038/nature13319

    Article  CAS  PubMed  Google Scholar 

  4. Lesur A, Domon B (2015) Advances in high-resolution accurate mass spectrometry application to targeted proteomics. Proteomics 15(5-6):880–890. doi:10.1002/pmic.201400450

    Article  CAS  PubMed  Google Scholar 

  5. Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Mechler A, Adda CG, Ang CS, Mathivanan S (2015) Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes. Oncotarget 6:15375–15396

    Article  PubMed  PubMed Central  Google Scholar 

  6. Onjiko RM, Moody SA, Nemes P (2015) Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo. Proc Natl Acad Sci U S A 112(21):6545–6550. doi:10.1073/pnas.1423682112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Lydic TA, Townsend S, Adda CG, Collins C, Mathivanan S, Reid GE (2015) Rapid and comprehensive 'shotgun' lipidome profiling of colorectal cancer cell derived exosomes. Methods 87:83–95. doi:10.1016/j.ymeth.2015.04.014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Habuka M, Fagerberg L, Hallstrom BM, Ponten F, Yamamoto T, Uhlen M (2015) The urinary bladder transcriptome and proteome defined by transcriptomics and antibody-based profiling. PLoS One 10(12):e0145301. doi:10.1371/journal.pone.0145301

    Article  PubMed  PubMed Central  Google Scholar 

  9. Uhlen M, Fagerberg L, Hallstrom BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson A, Kampf C, Sjostedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Ponten F (2015) Proteomics tissue-based map of the human proteome. Science 347(6220):1260419. doi:10.1126/science.1260419

    Article  PubMed  Google Scholar 

  10. No Authors Listed (2012) A home for raw proteomics data. Nat Methods 9(5):419

    Article  Google Scholar 

  11. Keerthikumar S, Chisanga D, Ariyaratne D, Al Saffar H, Anand S, Zhao K, Samuel M, Pathan M, Jois M, Chilamkurti N, Gangoda L, Mathivanan S (2016) ExoCarta: a Web-based compendium of exosomal cargo. J Mol Biol 428(4):688–692. doi:10.1016/j.jmb.2015.09.019

    Article  CAS  PubMed  Google Scholar 

  12. Keerthikumar S, Raju R, Kandasamy K, Hijikata A, Ramabadran S, Balakrishnan L, Ahmed M, Rani S, Selvan LD, Somanathan DS, Ray S, Bhattacharjee M, Gollapudi S, Ramachandra YL, Bhadra S, Bhattacharyya C, Imai K, Nonoyama S, Kanegane H, Miyawaki T, Pandey A, Ohara O, Mohan S (2009) RAPID: resource of Asian primary immunodeficiency diseases. Nucleic Acids Res 37(Database issue):D863–D867. doi:10.1093/nar/gkn682

    Article  CAS  PubMed  Google Scholar 

  13. Chisanga D, Keerthikumar S, Pathan M, Ariyaratne D, Kalra H, Boukouris S, Mathew NA, Saffar HA, Gangoda L, Ang CS, Sieber OM, Mariadason JM, Dasgupta R, Chilamkurti N, Mathivanan S (2016) Colorectal cancer atlas: an integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues. Nucleic Acids Res 44(D1):D969–D974. doi:10.1093/nar/gkv1097

    Article  PubMed  Google Scholar 

  14. Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Perez-Riverol Y, Reisinger F, Rios D, Wang R, Hermjakob H (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 41(Database issue):D1063–D1069. doi:10.1093/nar/gks1262

    Article  CAS  PubMed  Google Scholar 

  15. Vizcaino JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H (2016) 2016 update of the PRIDE database and its related tools. Nucleic Acids Res 44(D1):D447–D456. doi:10.1093/nar/gkv1145

    Article  PubMed  Google Scholar 

  16. Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL (2015) Trans-proteomic pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl 9(7-8):745–754. doi:10.1002/prca.201400164

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL (2013) The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res 12(1):162–171. doi:10.1021/pr301012j

    Article  CAS  PubMed  Google Scholar 

  18. Vizcaino JA, Foster JM, Martens L (2010) Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J Proteomics 73(11):2136–2146. doi:10.1016/j.jprot.2010.06.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA (2009) Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res 8(2):787–797. doi:10.1021/pr800538n

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Huttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL (2012) PASSEL: the PeptideAtlas SRMexperiment library. Proteomics 12(8):1170–1175. doi:10.1002/pmic.201100515

    Article  CAS  PubMed  Google Scholar 

  21. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. doi:10.1101/gr.1239303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ellis MJ, Gillette M, Carr SA, Paulovich AG, Smith RD, Rodland KK, Townsend RR, Kinsinger C, Mesri M, Rodriguez H, Liebler DC, Clinical Proteomic Tumor Analysis C (2013) Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. Cancer Discov 3(10):1108–1112. doi:10.1158/2159-8290.CD-13-0219

    Article  Google Scholar 

  23. Edwards NJ, Oberti M, Thangudu RR, Cai S, McGarvey PB, Jacob S, Madhavan S, Ketchum KA (2015) The CPTAC data portal: a resource for cancer proteomics research. J Proteome Res 14(6):2707–2713. doi:10.1021/pr501254j

    Article  CAS  PubMed  Google Scholar 

  24. Mathivanan S, Ji H, Tauro BJ, Chen YS, Simpson RJ (2012) Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry. J Proteomics 76:141–149. doi:10.1016/j.jprot.2012.06.031

    Article  CAS  PubMed  Google Scholar 

  25. Craig R, Cortens JP, Beavis RC (2005) The use of proteotypic peptide libraries for protein identification. Rapid Commun Mass Spectrom 19(13):1844–1850. doi:10.1002/rcm.1992

    Article  CAS  PubMed  Google Scholar 

  26. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372. doi:10.1038/nbt.1511

    Article  CAS  PubMed  Google Scholar 

  27. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551–3567. doi:10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

    Article  CAS  PubMed  Google Scholar 

  28. Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Bjorling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagne P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjerno K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Korner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Lobke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A (2008) Human proteinpedia enables sharing of human protein data. Nat Biotechnol 26(2):164–167. doi:10.1038/nbt0208-164

    Article  CAS  PubMed  Google Scholar 

  29. Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS, Pandey A (2009) Human proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res 37(Database issue):D773–D781. doi:10.1093/nar/gkn701

    Article  CAS  PubMed  Google Scholar 

  30. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A (2009) Human protein reference database—2009 update. Nucleic Acids Res 37(Database issue):D767–D772. doi:10.1093/nar/gkn892

    Article  CAS  PubMed  Google Scholar 

  31. Muthusamy B, Thomas JK, Prasad TS, Pandey A (2013) Access guide to human proteinpedia. Curr Protoc Bioinformatics 1:121. doi:10.1002/0471250953.bi0121s41

    Google Scholar 

  32. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Bjorling L, Ponten F (2010) Towards a knowledge-based human protein Atlas. Nat Biotechnol 28(12):1248–1250. doi:10.1038/nbt1210-1248

    Article  CAS  PubMed  Google Scholar 

  33. Marx V (2014) Proteomics: an atlas of expression. Nature 509(7502):645–649. doi:10.1038/509645a

    Article  CAS  PubMed  Google Scholar 

  34. Slotta DJ, Barrett T, Edgar R (2009) NCBI peptidome: a new public repository for mass spectrometry peptide identifications. Nat Biotechnol 27(7):600–601. doi:10.1038/nbt0709-600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Csordas A, Wang R, Rios D, Reisinger F, Foster JM, Slotta DJ, Vizcaino JA, Hermjakob H (2013) From peptidome to PRIDE: public proteomics data migration at a large scale. Proteomics 13(10-11):1692–1695. doi:10.1002/pmic.201200514

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Shivakumar Keerthikumar .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Keerthikumar, S., Mathivanan, S. (2017). Proteomic Data Storage and Sharing. In: Keerthikumar, S., Mathivanan, S. (eds) Proteome Bioinformatics. Methods in Molecular Biology, vol 1549. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6740-7_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6740-7_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6738-4

  • Online ISBN: 978-1-4939-6740-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics