Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis

Nature Biotechnology volume 35, pages 409–412 (2017)Cite this article

Subjects

Access through your institution
Buy or subscribe

To the Editor:

Improvements in next-generation proteomics, including instrumentation1,2, sample preparation, and computational analysis3,4, have generated large amounts of data that cover protein profiling, post-translational modifications, and protein–protein interactions5,6. The first draft of the human proteome, for example, made use of 2,000 (ref. 6) and 16,000 (ref. 5) raw files. Proteomics now calls for a uniform online pipeline that can host millions of data sets with the same quality standards, analyze hundreds to thousands of experiments, and integrate multi-dimensional omics data for knowledge mining and hypothesis generation to disseminate proteomics to the scientific community. Here, we describe Firmiana (V1.0) (http://www.firmiana.org/), a one-stop proteomic data processing and integrated omics analysis cloud platform that allows scientists to deposit mass spectrometry (MS) raw files, perform proteome identification and quantification online, carry out bioinformatics analyses, extract knowledge, and visualize results using a biologist-friendly web interface without the need for programming expertise.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Functional modules and capability in large-scale proteomics data processing in the Firmiana workflow.
Figure 2: Data/knowledge mining and high performance computing in Firmiana.

References

  1. Olsen, J.V. et al. Mol. Cell. Proteomics 8, 2759–2769 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Nagaraj, N. et al. Mol. Cell. Proteomics 11, 013722 (2012).

    Article  Google Scholar 

  3. Cox, J. & Mann, M. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article  CAS  PubMed  Google Scholar 

  4. Röst, H.L. et al. Nat. Biotechnol. 32, 219–223 (2014).

    Article  PubMed  Google Scholar 

  5. Wilhelm, M. et al. Nature 509, 582–587 (2014).

    Article  CAS  PubMed  Google Scholar 

  6. Kim, M.S. et al. Nature 509, 575–581 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Vaudel, M., Barsnes, H., Berven, F.S., Sickmann, A. & Martens, L. Proteomics 11, 996–999 (2011).

    Article  CAS  PubMed  Google Scholar 

  8. Vaudel, M. et al. Nat. Biotechnol. 33, 22–24 (2015).

    Article  CAS  PubMed  Google Scholar 

  9. Tyanova, S. et al. Nat. Methods 13, 731–740 (2016).

    Article  CAS  PubMed  Google Scholar 

  10. Sturm, M. et al. BMC Bioinformatics 9, 163 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Ma, B. et al. Rapid Commun. Mass Spectrom. 17, 2337–2342 (2003).

    Article  CAS  PubMed  Google Scholar 

  12. Vizcaíno, J.A. et al. Nat. Biotechnol. 32, 223–226 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Martens, L. et al. Proteomics 5, 3537–3545 (2005).

    Article  CAS  PubMed  Google Scholar 

  14. Nesvizhskii, A.I. Nat. Methods 11, 1114–1125 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Deutsch, E.W., Lam, H. & Aebersold, R. EMBO Rep. 9, 429–434 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Pedrioli, P.G. Methods Mol. Biol. 604, 213–238 (2010).

    Article  CAS  PubMed  Google Scholar 

  17. Jagtap, P.D. et al. J. Proteome Res. 13, 5898–5908 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Shteynberg, D. et al. Mol. Cell. Proteomics 10, 007690 (2011).

    Article  Google Scholar 

  19. Zhang, W. et al. Proteomics 12, 3475–3484 (2012).

    Article  CAS  PubMed  Google Scholar 

  20. Ding, C. et al. Mol. Cell. Proteomics 12, 2370–2380 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kent, W.J. et al. Genome Res. 12, 996–1006 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Cahan, P. et al. Cell 158, 903–915 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work is supported by National International Cooperation Grant (2014DFB30010) (J.Q.); National Program on Key Basic Research Project (973 Program, 2014CBA02001 (W.L.); 2014CBA02002 (Q.Z.); 2014CBA02004 (L.S., M.L.)); Chinese Ministry of Science and Technology (2016YFA0502500) (C.D.); National High-tech R&D Program of China (863 program, 2015AA020108 (T.S., X.X.); 2012AA020201 (C.D.)); National Program on Key Basic Research Project (973 Program, 2012CB910300) (J.Q.); National International Cooperation Grant (2012DFB30080 (C.D., J.Q.)); National Natural Science Foundation of China (31200582 (C.D.); 31170779 (J.Q.); 31200992 (W.L.); 31270822 (C.D.)) and Beijing Natural Science Foundation (5132012 (C.D.); Z131100005213003 (J.Q.)) and Shanghai 111 Project (B14019 (T.S.)).

Author information

Author notes

  1. Jinwen Feng, Chen Ding, Naiqi Qiu, Xiaotian Ni and Dongdong Zhan: These authors have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China

    Jinwen Feng, Chen Ding, Naiqi Qiu, Xiaotian Ni, Dongdong Zhan, Wanlin Liu, Xia Xia, Lei Song, Quan Zhou, Mi Lai, Gaigai Guo, Weimin Zhu & Jun Qin

  2. The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China

    Jinwen Feng, Naiqi Qiu, Xiaotian Ni, Dongdong Zhan, Peng Li, Bingxin Lu & Tieliu Shi

  3. State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai, China

    Chen Ding & Jun Qin

  4. State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China

    Qi Zhao, Peng Nie & Jian Ren

Authors
  1. Jinwen Feng
    View author publications

    Search author on:PubMed Google Scholar

  2. Chen Ding
    View author publications

    Search author on:PubMed Google Scholar

  3. Naiqi Qiu
    View author publications

    Search author on:PubMed Google Scholar

  4. Xiaotian Ni
    View author publications

    Search author on:PubMed Google Scholar

  5. Dongdong Zhan
    View author publications

    Search author on:PubMed Google Scholar

  6. Wanlin Liu
    View author publications

    Search author on:PubMed Google Scholar

  7. Xia Xia
    View author publications

    Search author on:PubMed Google Scholar

  8. Peng Li
    View author publications

    Search author on:PubMed Google Scholar

  9. Bingxin Lu
    View author publications

    Search author on:PubMed Google Scholar

  10. Qi Zhao
    View author publications

    Search author on:PubMed Google Scholar

  11. Peng Nie
    View author publications

    Search author on:PubMed Google Scholar

  12. Lei Song
    View author publications

    Search author on:PubMed Google Scholar

  13. Quan Zhou
    View author publications

    Search author on:PubMed Google Scholar

  14. Mi Lai
    View author publications

    Search author on:PubMed Google Scholar

  15. Gaigai Guo
    View author publications

    Search author on:PubMed Google Scholar

  16. Weimin Zhu
    View author publications

    Search author on:PubMed Google Scholar

  17. Jian Ren
    View author publications

    Search author on:PubMed Google Scholar

  18. Tieliu Shi
    View author publications

    Search author on:PubMed Google Scholar

  19. Jun Qin
    View author publications

    Search author on:PubMed Google Scholar

Corresponding authors

Correspondence to Chen Ding, Tieliu Shi or Jun Qin.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Notes 2 and 3, Supplementary Table 1 and Supplementary Methods (PDF 432 kb)

Supplementary Figures 1–24 (PDF 120002 kb)

Supplementary Note 1, User Manual (DOCX 32 kb)

Supplementary Video

Instructions for Firmiana (MP4 61849 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Feng, J., Ding, C., Qiu, N. et al. Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis. Nat Biotechnol 35, 409–412 (2017). https://doi.org/10.1038/nbt.3825

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.3825

This article is cited by

Search

Advanced search

Quick links

Nature Briefing AI and Robotics

Sign up for the Nature Briefing: AI and Robotics newsletter — what matters in AI and robotics research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: AI and Robotics