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.

Our paper A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides has been accepted for publication by Nature Communications. Congratulations and please cite this paper if you used pLink 2.

Cite us

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Zhen-Lin Chen, Jia-Ming Meng, Yong Cao, Ji-Li Yin, Run-Qian Fang, Sheng-Bo Fan, Chao Liu, Wen-Feng Zeng, Yue-He Ding, Dan Tan, Long Wu, Wen-Jing Zhou, Hao Chi, Rui-Xiang Sun, Meng-Qiu Dong & Si-Min He. Nature Communications. July 30, 2019. [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.

Notice

• The expiration date of pLink 2.3.11 is set on Jan. 10, 2025.
• If RAW file read required, MSFileReader, 3.0 SP2 or a lower version, both 32 bit and 64 bit, need be installed first.
  • If you have problem to run pLink 2 on Windows 7, please see this issue. Re-install MSFileReader using "Run as administrator".
• .NET framework 4.5 or a higher version is required.
• Java is also required for quantitation.

pLink Release Notes

Version 2.3.11 - March 28 2022

• Change the website to http://pfind.org from http://pfind.ict.ac.cn.
• Add the self-service registration website http://i.pfind.org.
• The license for version 2.3.10 is still valid for version 2.3.11. The same expiration date is Jan. 10, 2025.
• If you have problem to run pLink 2 on Windows 7, please see this issue. Re-install MSFileReader using "Run as administrator".

Version 2.3.10 - January 12 2022

• Fixed a major bug in calculating E-value that causes software to crash, thank you Olexandr Dybkov and Liu Lab who reported.
• Changed the format of 'Precursor_Mass' and 'Peptide_Mass' in the report to decimal, thank you @IwanParf.
• Fixed several other bugs.
• All users are recommended to update to this version if required.
• A new license is required for this version, but we have extended the license validity to three years. This means you can use pLink 2.3.10 until 2025.1.10 without worrying about expiration.
• If you have problem to run pLink 2 on Windows 7, please see this issue. Re-install MSFileReader using "Run as administrator".

  Version 2.3.9 - January 7 2020

• Fixed a pParse bug, thank you lili.
• Fixed a fasta reading bug, thank you @vladtheimpalerSr.
• Updated the user guide, please read it before installation.
• All users using version 2.3.8 are recommended to update to this version.
• License for version 2.3.8 is still valid for this version.
• If you have problem to run pLink 2.3.9 on Windows 7, please see this issue.

  Version 2.3.8 - December 27 2019

• Happy New Year 2020!
• Fixed a quantitation bug on French Edition of Windows.
• Updated the configuration for cross-linker.
• Updated pLabel for MS-cleavable cross-linked spectra annotation.
• Updated the user guide, please read it before installation.
• A new license is required for this version, but we have extended the license validity to three years. This means you can use pLink 2.3.8 until 2023 without worrying about expiration.

  Version 2.3.7 - November 5 2019

• Fixed a bug when open pLabel.
• License for version 2.3.5 is still valid for this version.

  Version 2.3.6 - September 30 2019

• Congratulations! Our paper of pLink 2 is finally published, and please cite this paper if you used pLink 2.
• Fixed a bug when register the software.
• Fixed a bug when showing the symbol of β in pLabel.
• Disabled the SUMO identification flow temporarily, as we are optimizing and testing it. This feature will be available as soon as possible.
• Updated the lists of modifications and enzymes.
• Updated the GUI.
• License for version 2.3.5 is still valid for this version.

  Version 2.3.5 - December 29 2018

• Happy New Year 2019, and please see greetings from your pLink developers!
• Fixed a bug when infer proteins from peptides, thank you @zrpeak.
• Fixed a bug when the database is small.
• Fixed a bug when save a disulfide bond search task.
• Fixed a bug in modification tab of pConfig.
• Add a warning when combineSS.exe failed.
• Updated expiration time to January 1 2020.
• A new license is required since this version and will be valid until January 1 2020.

  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.