Skip to main content
SpringerLink
Log in
Book cover

Brazilian Symposium on Bioinformatics

BSB 2021: Advances in Bioinformatics and Computational Biology pp 125–130Cite as

FluxPRT: An Adaptable and Extensible Proteomics LIMS

  • Conference paper
  • First Online:

  • 398 Accesses

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13063))

Abstract

Proteomics is a fundamental research area that focuses on large-scale protein analysis. Data generated from experimental approaches in proteomics is becoming increasingly complex to organize and manage. Laboratory Information Management Systems (LIMS) allow this data to be managed in a flexible and efficient way. However, most LIMS have a high cost and are directed at specific needs. This work introduces FluxPRT, a comprehensive and adaptable proteomics workflow-based LIMS supported by an interactive web page guide aimed at assisting novice researchers in a proteomics lab. FluxPRT is available at http://www.flux2.luar.dcc.ufmg.br and provides an important tool to assist preotemics research.

Supported by Capes. Fellowship: 88887.517813/2020-00.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   44.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   59.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Learn about institutional subscriptions

References

  1. Brown, K.A., Melby, J.A., Roberts, D.S., Ge, Y.: Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev. Proteomics 17(10), 719–733 (2020). https://doi.org/10.1080/14789450.2020.1855982

    Article  CAS  PubMed  Google Scholar 

  2. Cheng, K., et al.: Metalab: an automated pipeline for metaproteomic data analysis. Microbiome 5(1), 1–10 (2017). https://doi.org/10.1186/s40168-017-0375-2

    Article  Google Scholar 

  3. Dupree, E.J., Jayathirtha, M., Yorkey, H., Mihasan, M., Petre, B.A., Darie, C.C.: A critical review of bottom-up proteomics: the good, the bad, and the future of this field. Proteomes 8(3), 14 (2020). https://doi.org/10.3390/proteomes8030014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Faria-Campos, A.C., Hanke, L.A., Batista, P.H., Garcia, V., Campos, S.V.: An innovative electronic health record system for rare and complex diseases. BMC Bioinform. 16(19), 1–8 (2015). https://doi.org/10.1186/1471-2105-16-S19-S4

    Article  Google Scholar 

  5. Hinton, M.: LIMS in the manufacturing environment. Lab. Autom. Inf. Manage. 31(2), 109–113 (1995). https://doi.org/10.1016/1381-141X(95)80027-Z

    Article  CAS  Google Scholar 

  6. Lermyte, F., Tsybin, Y.O., O’Connor, P.B., Loo, J.A.: Top or middle? up or down? toward a standard lexicon for protein top-down and allied mass spectrometry approaches. J. Am. Soc. Mass Spectrometry 30(7), 1149–1157 (2019). https://doi.org/10.1007/s13361-019-02201-x

    Article  CAS  Google Scholar 

  7. Martínez-Bartolomé, S., Binz, P.A., Albar, J.P.: The minimal information about a proteomics experiment (MIAPE) from the proteomics standards initiative. In: Plant Proteomics, pp. 765–780. Springer (2014). https://doi.org/10.1007/978-1-62703-631-3_53

  8. Melo, A., Faria-Campos, A., DeLaat, D.M., Keller, R., Abreu, V., Campos, S.: Sigla: an adaptable LIMS for multiple laboratories. BMC Genomics 11(5), 1–8 (2010). https://doi.org/10.1186/1471-2164-11-S5-S8

    Article  Google Scholar 

  9. Vizcaíno, J.A., et al.: Proteomexchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnol. 32(3), 223–226 (2014). https://doi.org/10.1038/nbt.2839

    Article  CAS  Google Scholar 

  10. Wen, B., Zhou, R., Feng, Q., Wang, Q., Wang, J., Liu, S.: Iquant: an automated pipeline for quantitative proteomics based upon isobaric tags. Proteomics 14(20), 2280–2285 (2014). https://doi.org/10.1002/pmic.201300361

    Article  CAS  PubMed  Google Scholar 

  11. Wilkins, M.R., et al.: Information management for proteomics: a perspective. Expert Rev. Proteomics 5(5), 663–678 (2008). https://doi.org/10.1586/14789450.5.5.663

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Programa de Pós -Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    Elizabeth Regina Alfaro-Espinoza

  2. Laboratório de Universalização de Acesso, Departamento de Ciência da Computação, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    Elizabeth Regina Alfaro-Espinoza, Alessandra C. Faria-Campos & Sérgio Vale Aguiar Campos

  3. Programa de Pós-Graduação em Ciência da Computação, Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil

    Lucas Ferreira Paiva

  4. Laboratório de Proteômica e Bioquímica de Proteınas, Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil

    Elizabeth Regina Alfaro-Espinoza & Maria Cristina Baracat-Pereira

  5. Laboratório de Bioengenharia - Instituto Nacional de Metrologia, Qualidade e Tecnologia, Viçosa, Brazil

    Alessandra C. Faria-Campos

Authors
  1. Elizabeth Regina Alfaro-Espinoza
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lucas Ferreira Paiva
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alessandra C. Faria-Campos
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Maria Cristina Baracat-Pereira
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sérgio Vale Aguiar Campos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Elizabeth Regina Alfaro-Espinoza .

Editor information

Editors and Affiliations

  1. Leipzig University, Leipzig, Sachsen, Germany

    Peter F. Stadler

  2. University of Brasília, Brasilia, Brazil

    Maria Emilia M. T. Walter

  3. CINVESTAV, Irapuato, Mexico

    Maribel Hernandez-Rosales

  4. Universidade de Brasilia, Brasilia, Brazil

    Marcelo M. Brigido

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Alfaro-Espinoza, E.R., Paiva, L.F., Faria-Campos, A.C., Baracat-Pereira, M.C., Campos, S.V.A. (2021). FluxPRT: An Adaptable and Extensible Proteomics LIMS. In: Stadler, P.F., Walter, M.E.M.T., Hernandez-Rosales, M., Brigido, M.M. (eds) Advances in Bioinformatics and Computational Biology. BSB 2021. Lecture Notes in Computer Science(), vol 13063. Springer, Cham. https://doi.org/10.1007/978-3-030-91814-9_12

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-91814-9_12

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-91813-2

  • Online ISBN: 978-3-030-91814-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation