Poster Presentation 23rd Annual Lorne Proteomics Symposium 2018

Lazyprot: a comprehensive software for the bioinformatic processing and pre-processing of proteomic data (#93)

Jeremy Potriquet 1 , John Miles 1 , Jason Mulvenna
  1. James cook university, Smithfield, QLD, Australia

In recent years, the number of technologies and instruments available and the field of applications for mass spectrometry have grown exponentially and with it the need for application software able to process with this tremendous amount of data generated. In parallel, the latest effort pulled by industry to make mass spectrometry affordable and the interface usable even by neophytes have widen the range of users and related knowledge about the omics techniques.

When it comes to data processing, often considered a bottle neck of many experiments, new tools for the analysis and interpretation of data are released regularly by industry and the scientific community [1, 2], however a regularly forgotten side of it is the pre- and post-processing of the data to be inputted or outputted by such elaborated pipelines. To format correctly or extract useful information from omics analysis sometime the best option remains bioinformatics [3].

Without a proper support bioinformatics can very quickly become frustrating and requires a substantial time and effort investment before becoming useful. To overcome this, Lazyprot was designed to provide a comprehensive and versatile solution to common problems when dealing with bioinformatics data but also attempt to provide innovative tools for the processing of proteomics quantitation and more specifically the SWATH workflow.

Generation of proportionated venn diagrams, formatting and combination of fasta files, this tool also provides some solutions for mzML spectra representation and visual de novo sequencing as well as in silico Library generation for SWATH experiments and liquid chromatography retention time transposition from one system to another. All these tools are packaged in a Python language interface without dependencies or installation needed to make proteomic analysis as easy as possible.

  1. Deutsch EW, Mendoza L, Shteynberg D, et al. A Guided Tour of the Trans-Proteomic Pipeline. Proteomics. 2010;10(6):1150-1159. doi:10.1002/pmic.200900375.
  2. MacLean B, Tomazela DM, Shulman N, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 2010;26(7):966-968. doi:10.1093/bioinformatics/btq054.
  3. Cappadona S, Baker PR, Cutillas PR, Heck AJR, van Breukelen B. Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids. 2012;43(3):1087-1108. doi:10.1007/s00726-012-1289-8.