pFind Studio: a computational solution for mass spectrometry-based proteomics

Version history

The new expiration date is Dec.18, 2027. License since Version 3.2.1 still valid for this version.
Adding support for timsTOF pro, Astral instruments and FAIMS data.
Adding PFB/PFC data file format for efficient reading and writing.
Optimized the efficiency of data preprocessing against large-scale RAW file data.
[pParse] Improved precursor detection for low-abundance or incomplete isotopic clusters.
[pFind-GUI] Adding a notification module for publishing messages.

The new expiration date is Jan. 10, 2026. License since version 3.1.3 is still valid for this version.
Optimized the workflow of searching against huge proteome database files.
Optimized the function of blind search, which has been used in pChem.
Fixed some bugs in the previous version and changed a few descriptions in the result files.

The new expiration date is Jan. 10, 2023. License since version 3.1.3 is still valid for this version.
[Kernel] Optimized the performance of the restricted search mode on low resolusion MS data.
[Kernel] Fixed the bug when processing the MS/MS data with negative charge mode.
[GUI] Adding the multi-process-mode when running pParse.

The new expiration date is Dec. 31, 2019. License since version 3.1.3 is still valid for this version.
Add the description of the result file in the installation folder.
The maximum number of fixed modifications is set as 20, which is not limited by the parameter settings.
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.
Updated 'modification.ini' based on the latest version of Unimod database (http://www.unimod.org)
Supported the MS data analysis with mzML format.
Add the description of the result file in the installation folder.

[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.
[Kernel] [IMPORTANT] Fixed a bug of processing large protein databases (> 4GB).
[pFind-GUI] User must click the 'Save' button and then click the 'Start' button to start a search.
[pFind-GUI] Changed the default parameters of TMT-6plex and TMT-10plex
[pFind-GUI] Fixed a bug of saving parameter files in processing MS2 quantitation
[pBuild] Added the feature of reporting all retention times of the identified peptides.
[pBuild] Added the feature of reporting all matched b/y ions of the identified PSMs.
[pBuild] Fixed some typos in the interface.
[pBuild] Optimized the demonstration of the identification with MGF files.
[Kernel] Output the procedure of generating peptide candidates when the program is running.
[Kernel] Output a new result file named "pFind-Filtered.spectra", which contains the target PSMs within the given FDR threshold, e.g., 0.01.
[pParse] Fixed a bug of output the .csv file of large MS/MS data (it may contain multiple headers).
[pParse] Supported the export of precursors of low resoluation MS1 data (do not call pParse algorithm but only output the corresponding .pf1 and .pf2 files for the following database search).
License since version 3.1.3 is still valid for this version.

[IMPORTANT] The new expiration date is August 1, 2019. As the license module is updated, please applied for the new license file.
[IMPORTANT] Fixed a bug when setting the workspace directory.
[IMPORTANT] Fixed a bug of the license module which may affect the registration of some users using Win 10 system.
Fixed a text error in the pFind.spectra file.
Added a warning when users choose "open search" for low resolution MS/MS data.
Added the option of retrieving all PSMs by any given protein accession number in pBuild.
Optimized the appearance of the welcome page.
Optimized the option of comparing two PSMs.
Optimized the naming rule of the temporary files output by the kernel program.