Introduction and Download Website

        ProVerB is a database searching algorithm to identify peptides from tandem mass spectrometry (MS/MS), developed by proteomics research group in Jinan University, China. The ProVerB program (source code) are available below:



Windows 32-bit Download Download
Windows 64-bit Download Download
Source Code Download

User Interface and Usage

  ProVerB has a very friendly graphical user interface. This version of ProVerB is programmed by Matlab and C, it can be compiled in various systems with Matlab Running environment and C compiler (Windows and Linux). 64-bit operating system is highly recommended for better performance and higher capacity. Running ProVerB.m in Matlab or ProVerB.exe in windows should load the parameter collection interface:  

Step by step to use:
Step 1 select correct database type of public sample database (1) and browse the fasta format database file (11).
Step 2 select the enzyme used in experimental protein digestion (2).
Step 3 set the missed cleave sites (3).
Step 4 set the parent ion tolerance (4) and unit (5) according to instruments type.
Step 5 set the fragment ion tolerance (6) according to instruments type.
Step 6 Add the fixed modifications (7,8) and variable modifications (9,10) you want to search.
Step 7 browse the father folder of MS/MS data folder (12). ProVerB supports dta format files only.
Step 8 browse to set the results folder (13).
Step 9 You can start the run by clicking "start search"(14) or reset all fields by clicking "reset"(15)

Format of the output file:
The output is in csv format. The top 10 score peptides of each MS/MS are exported in the result file:
[dta file name],[rank],[number of theoretical fragment peaks],[number of matched peaks],[number of the consecutive matches in the theoretical spectrum],[number of the consecutive matches in the experimental spectrum],[S score], [peptide sequence],[missed cleave sites],[calc M+H+],[experimental M+H+],[charge],[protein number for peptide sequnce]

Here is an example:

Note: protein annotation information of protein number can be found in databaselist.txt.

Format of the modification configure file(modification.txt):
The modification.txt file is in excel format by Tab separator, Each line is a modification configure information:
[modification name] [modified amino acid] [modification average molecular weight] [modification molecular structure] [mono molecular weight]
Carbamidomethyl (C) C 57.0513 H(3) C(2) N O 57.021464
If you want to add a new modification, please modify this file by the above format.

Trainning Dataset for Algorithm's Parameter

   The total protein sample from S. pneumoniae D39 was performed in Orbitrap-LTQ and identified by ProVerB. This dataset contains more than 270,000 spectra and served as training dataset for parameters of the ProVerB model.
Download this dataset:
                                      Raw Data
                                      Dta Format Data
                                      Database File(.fasta)


Chuan-Le Xiao, Xiao-Zhou Chen, Yang-Li Du, Xuesong Sun, Gong Zhang, and Qing-Yu He.Binomial Probability Distribution Model-Based Protein Identification Algorithm for Tandem Mass Spectrometry Utilizing Peak Intensity Information
Journal of Proteome Research 2013 12 (1), 328-335. [Download]


ProVerB is developed and programmed by Chuan-Le Xiao,Gong Zhang and Yang-Li Du. For any questions, suggestions, problem reports and new function requests please contact: xiaochuanle[at], zhanggong[at] and du_yangli[at]