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README.md

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@@ -10,28 +10,38 @@ The paper of Open-pFind has been uploaded to the preprint server of bioRxiv: <a
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## Cite us
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1. <a href="https://www.biorxiv.org/content/early/2018/03/20/285395">Open-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics</a></h6>
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Hao Chi, Chao Liu, Hao Yang, Wen-Feng Zeng, Long Wu, Wen-Jing Zhou, Xiu-Nan Niu, Yue-He Ding, Yao Zhang, Rui-Min Wang, Zhao-Wei Wang, Zhen-Lin Chen, Rui-Xiang Sun, Tao Liu, Guang-Ming Tan, Meng-Qiu Dong, Ping Xu, Pei-Heng Zhang, Si-Min He. <b>BioRxiv</b>, Mar. 20, 2018. </a></p>
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Hao Chi, Chao Liu, Hao Yang, Wen-Feng Zeng, Long Wu, Wen-Jing Zhou, Xiu-Nan Niu, Yue-He Ding, Yao Zhang, Rui-Min Wang, Zhao-Wei Wang, Zhen-Lin Chen, Rui-Xiang Sun, Tao Liu, Guang-Ming Tan, Meng-Qiu Dong, Ping Xu, Pei-Heng Zhang, Si-Min He. <b>BioRxiv</b>, Mar. 20, 2018. </a></p>
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## Downloads
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pFind 3 is currently free to use. **[Download pFind 3.1.4](http://pfind.ict.ac.cn/file/3.1/pFind3.1_Setup_20181121.exe)**.
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pFind 3 is currently free to use. **[Download pFind 3.1.5](http://pfind.ict.ac.cn/file/3.1/pFind3.1_Setup_20190124.exe)**.
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Please download and read [user_guide.pdf](http://pfind.ict.ac.cn/file/3.1/pFind%203%20UserGuide.pdf) before download and use pFind 3.
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Notice:
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<p>* The expiration date is set on <b>Aug. 1, 2019</b>.</p>
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<p>* The expiration date is set on <b>Dec. 31, 2019</b>.</p>
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<p>* If RAW file read required, <a href="https://thermo.flexnetoperations.com/control/thmo/product?plneID=632401" target="_blank">MSFileReader 3.0</a> or a higher version need be installed first.</p>
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<p>* <a href="https://www.microsoft.com/zh-cn/download/details.aspx?id=30653" target="_blank">.NET framework 4.5 </a> or a higher version is required.</p>
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<p>* pFind can support Windows 7 or higher, and the operating system should be <b>64-bit</b>.</p>
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<p>* For Windows 7 operating system, please run the setup program under administrator authority. If any one program cannot properly run after the installation, please try to right click on the program shortcut or the .exe file, and click on "Run as administrator".</p>
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If you have any questions about it, please contact [[email protected].](mailto:[email protected])
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If you have any questions about it, please contact [[email protected]](mailto:[email protected]).
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Online discussion: [https://github.com/pFindStudio/pFind3/issues](https://github.com/pFindStudio/pFind3/issues), see [github.pdf](http://pfind.ict.ac.cn/file/github.pdf) for usage.
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## pFind Release Notes
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#### Version 3.1.5 - Jan. 24 2019
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* The new expiration date is Dec. 31, 2019. License since version 3.1.3 is still valid for this version.
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* Add the description of the result file in the installation folder.
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* The maximum number of fixed modifications is set as 20, which is not limited by the parameter settings.
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* Changed the strategy of protein inference in the restricted search mode: semi-/non-specifically digested peptides were also considered in the procedure of protein inference.
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* Updated 'modification.ini' based on the latest version of Unimod database [(http://www.unimod.org)] (http://www.unimod.org)
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* Supported the MS data analysis with mzML format.
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* Add the description of the result file in the installation folder.
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#### Version 3.1.4 - Nov. 21 2018
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* [pFind-GUI] [IMPORTANT] Added a new quantitation method of "Report-Intensity", which is the same as the common identification workflow but call pQuant to calculate the intensity of each peptide afterwards.
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* [Kernel] [IMPORTANT] Fixed a bug of processing large protein databases (> 4GB).

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