pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
images/MSFileReader
README.md

README.md

pLink 2

pLink® is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.

pLink 2 is developed as an upgrade of pLink 1. Compared with pLink 1, pLink 2 provides a graphical user interface, and is ~40 times faster with a newly designed index structure. There are also some improvements in the precision.

Cite us

  1. Identification of cross-linked peptides from complex samples. Bing Yang, Yan-Jie Wu, Ming Zhu, Sheng-Bo Fan, Jin-Zhong Lin, Kun Zhang, Shuang Li, Hao Chi, Yu-Xin Li, Hai-Feng Chen, Shu-Kun Luo, Yue-He Ding, Le-Heng Wang, Zhi-Qi Hao, Li-Yun Xiu, She Chen, Ke-Qiong Ye, Si-Min He and Meng-Qiu Dong. Nature Methods. July 08, 2012. [abstract]

  2. Mapping native disulfide bonds at a proteome scale. Shan Lu, Sheng-Bo Fan, Bing Yang, Yu-Xin Li, Jia-Ming Meng, Long Wu, Pin Li, Kun Zhang, Mei-Jun Zhang, Yan Fu, Jin-Cai Luo, Rui-Xiang Sun, Si-Min He, Meng-Qiu Dong. Nature Methods. Feb. 9, 2015. [abstract]

Downloads

Please download and read user_guide.pdf before download and use pLink 2.

pLink 2 is currently free to use. Download pLink 2.3.

If you have any questions about it, please contact pLink@ict.ac.cn.

Online discussion: https://github.com/pFindStudio/pLink2/issues, see github.pdf for usage.

pLink Release Notes

Version 2.3.4 - September 5 2018

  • Fixed a bug when searching super long peptides. Please note that the min length of peptides cannot be shorter than 4aa and the max length of peptides cannot be longer than 120aa.
  • Fixed a bug when the unit of fragment tolerance is Da.
  • Fixed a bug when activating software in Windows 7.
  • Merged the SS flow and the SS_0 flow in disulfide bonds identification.
  • Provided the global FDR estimation for intra-protein and inter-protein cross-links.
  • Supported lower case amino acids in fasta file.
  • Added a warning when the path of pf2 file is invalid.
  • Improved GUI usability.
  • Updated expiration time to August 1 2019.
  • A new license is required since this version and will be valid until August 1 2019.

Version 2.3.3 - May 30 2018

  • Fixed a bug when labeling the -NH3/-H2O peaks in pLabel.
  • Fixed a bug when drawing the FDR curve.
  • Fixed a bug when running on Windows 10 Build 1803.
  • Improved the spectra preprocessing algorithm.
  • License since version 2.3.0 is still valid for this version.

Version 2.3.2 - April 4 2018

  • Fixed a bug when the m/z of a peak is negative.
  • Fixed a bug when the result is empty.
  • Fixed a bug when computing E-value with SS_0 linker.
  • Fixed a bug when clicking HELP button in pLabel.
  • Corrected the mono mass of SS_0 linker.
  • Found solution to pLabel's annotation problem on non-Chinese Edition of Windows.
  • License since version 2.3.0 is still valid for this version.

Version 2.3.1 - February 9 2018

  • Fixed a bug on French Edition of Windows.
  • License for version 2.3.0 is still valid for this version.

Version 2.3.0 - January 31 2018

  • Fixed the decimal point bug on French Edition of Windows.
  • Fixed a bug on some Windows 10 Pro.
  • Fixed bugs when configuring Enzymes and Quantifications.
  • Fixed pLabel annotation problem with MGF extracted by PD.
  • Disabled the requirement of administrative privileges.
  • Improved software activation methods.
  • Improved robustness when searching against *.fasta file containing non-alphabet characters.
  • Improved GUI usability.
  • Added validity check when configuring meta data.
  • Extended the max missed cleavages to 5.
  • Extended quantification support to BS3 labeling.
  • Changed the default variable modification when linker SS used.
  • Removed pBuild folder in results.
  • Updated the user guide.

Version 2.2.1649 - December 30 2017

  • First public beta version.