Standalone version

Installation

To use the standalone version of PepQuery2, first install it on your computer:

You must have Java 1.8 or newer installed. To check your java version please open your terminal application and run the following command. If you do not have Java installed, follow these instructions.

java -version

Next go to download the standalone version of PepQuery here. After you download it, please uncompress it using the following command line and you will find a jar file in the package folder. The whole installation process typically only takes one or two minutes. Depending on where the file is downloaded you might need to adjust the path (see example below)

tar xvzf Downloads/pepquery-2.0.2.tar.gz (or tar xvzf pepquery-2.0.2.tar.gz)

If you want to run PepQuery with your own data you need to provide MS/MS data in MGF format, a reference protein database in FASTA format and a peptide, protein, DNA sequence or a pair of peptide and spectrum ID. We will not go into this here, so please refer to the official documantation for more information.

Identifying novel peptides

Let’s repeat the example from the Web Application section: Can you identify the novel peptide LVVVGADGVGK from the KRAS G12D mutation in the LUAD (lung adenocarcinoma), COAD (colon adenocarcinoma) and OV (ovarian cancer) datasets?

With the standalone version you can search all three datasets at the same time by running the following command:

java -jar pepquery-2.0.2/pepquery-2.0.2.jar -b CPTAC_LUAD_Discovery_Study_Proteome_PDC000153,CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111,CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118 -db gencode:human -o Desktop/pepquery_kras_g12d/ -i LVVVGADGVGK

So let’s take a closer look at the command line:

  • java -jar pepquery-2.0.2/pepquery-2.0.2.jar: Link to your PepQuery installment

  • -b CPTAC_LUAD_Discovery_Study_Proteome_PDC000153, CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111, CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118: This specifies the datasets you want to search in. Multiple datasets are seperated with a comma. A full list of datasets in the PepQueryDB is available with “java -jar pepquery-2.0.2/pepquery-2.0.2.jar -b show”.

  • -db gencode:human: Specifies the reference database.

  • -o Desktop/pepquery_kras_g12d/: Output folder where the results are saved.

  • -i LVVVGADGVGK: Input peptides. Multiple peptides would be seperated with a comma.

There are a lot more parameters that can be set in the standalone version which are listed here.

Results

The results will appear in your specified output folder. The main result file of PepQuery is the psm_rank.txt file. This file includes the detailed identification results for the input target peptide. You can open the psm_rank.txt file in excel and check how many PSMs passed the quality checks (confident = ‘Yes’).

For Result visualisation please refer to the official PepQuery visualisation.

Note

There are many other examples in the official PepQuery Demo.