Web Application

Preparation

You can use PepQuery through PepQuery Web. To use PepQuery Web, you don’t need to prepare the MS/MS data and protein reference database or install the PepQuery software. All you need to do is provide the target peptide/protein/DNA sequence which you want to identify.

Identifying novel peptides

Let’s start with an example from the PepQuery2 manuscript: Can you identify the novel peptide LVVVGADGVGK from the KRAS G12D mutation?

  • How many PSMs can you identify in the LUAD (lung adenocarcinoma), COAD (colon adenocarcinoma) and OV (ovarian cancer) datasets?

Note

You can also just play around with the Web Application and query different known or novel peptides/proteins in any of the datasets.

Parameters to set

Here is a list of parameters you can send in the Web Application. In italic you can find one input for the example above.

  • MS/MS dataset: select one MS/MS dataset which you want to search. CPTAC_TCGA_Colon_cancer_Proteome_PDC000111

  • Task type: novel or known peptide/protein identification. Novel peptide/protein

  • Target event: select the sequence class you provide (Peptide, protein and DNA sequences). Peptide sequence

  • Input peptide/protein/DNA sequence or a protein ID: For one search, only one sequence is accepted. LVVVGADGVGK

  • Reference database: a protein reference database. gencode_v34_human

  • Scoring algorithm: peptide spectrum scoring algorithm: Hyperscore and MVH are available and Hyperscore is recommended. Hyperscore

  • Fast searching mode: choose to use the fast mode for searching or not. In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. Yes

Results

After running your query you get the following results:

  1. Identification overview: A list of the major parameters used in PepQuery including the command line to run it on the standalone version.

  2. Identification results: Overview of the PSMs with confident matches highlighted in green. An overview of the columns can be found here <http://pepquery.org/document.html#saoutput>_.

  3. Spectrum annotation: When you click on a PSM in the identification result you can see the corresponding spectrum. Additionally, you can look at the spectra from the best PSM in the reference database and the unrestricted modification-based search.

  4. Sample information: In theory you can find the sample information for the selected row here. However this has never worked for me so far.