PST: parallel simulation tool to study open search methods for the identification of peptides with post-translational modifications
About PST |
Tandem mass spectrometry is now the method of choice in large-scale proteomic study. Nowadays, there are three types of method for peptide identification based on the mass spectrometry data, i.e., database search, de novo sequencing and library search. Database search is predominant for its efficiency and robustness. After decades' development, more and more spectra with post-translational modifications can be identified using open search methods, such as spectrum-based open search [1] and tag-based open search [2].
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Related Publication |
J. Dai*, F. Yu*, C. Zhou, and W. Yu. *Contributed equally to this work. [1] J. M. Chick, D. Kolippakkam, D. P. Nusinow, B. Zhai, R. Rad, E. L. Huttlin, and S. P. Gygi, “A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides,” Nature Biotechnology, vol. 33, no. 7, pp. 743– 749, 2015. |
Where to download PST |
Source code (updated 22 Mar 2018):
PST_src.zip Data plotting (updated 18 Dec 2019):
REALDATA_Process.zip |
Environment configuration |
Please install Python 3 and NumPy to use this tool. |
How to use it |
Please change the directory to the root of the package before starting simulations. |