Google Summer of Code 2021 | Work Report

Mohamed Soudy
3 min readAug 20, 2021



Alfaro, J., Sinha, A., Kislinger, T. et al. Onco-proteogenomics: cancer proteomics joins forces with genomics. Nat Methods 11, 1107–1113 (2014).

LC/MS is a hyphenated technique, which combines the separating power of High-Performance Liquid Chromatography (HPLC), with the detection power of mass spectrometry. Mass Spectrometry is a wide-ranging analytical technique, which involves the production and subsequent separation and identification of charged species.

The project is developed as a standalone shiny app that requires the Extracted Spectra as Mascot Generic Format (MGF) and the Database as FASTA file.

Graphical User Interface (GUI)

Main page for the application

The application performs multiple functionalities as the identification or the regular search of the proteomics database using X! Tandem search engine, Furthermore, the application visualizes and report the results to the user in a handy way including the generation of identified spectra, peptides, proteins, and Post Translational Modifications (PTMs).

The application allows the user to enter a database and generates a database that contains the mutations of each sequence according to the six-frame translation.

Then the application performs an iterative database search to identify both regular peptides from the traditional search and mutated peptides from the search of mutated database that may lead to the identification of novel peptides.

Upload Page

The upload page is designed to retrieve the information regarding the Mass spectrometer output file ex: (MGF, RAW) and the database file in FASTA format the user can also change the search setting using the file default_param.xml with and customize the search parameters.

Search Page

The Search page reports the number of spectra in the input file, then applies the iterative search using the traditional and mutated database and returns the annotated results of spectra, peptides, proteins, and ptms.

Identified Spectra

Identified Peptides

Identified Proteins

Identified PTMs

Visualization Page

The Visualization page shows the annotated spectra of each identified peptide including the MS/MS results reporting the m/z ratio on the x-axis and the intensities on the y-axis.

Remove identification Page

The Remove identification page excludes the identified spectra from the regular database search and writes a new spectral file to be used in the iterative search process for other databases.