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

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

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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.

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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.

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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
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  2. Chen Ding
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  7. Xia Xia
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  18. Tieliu Shi
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  19. Jun Qin
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Corresponding authors

Correspondence to Chen Ding, Tieliu Shi or Jun Qin.

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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)

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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

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