Poster Presentation 23rd Annual Lorne Proteomics Symposium 2018

A web-based quality control tool for the bench marking of proteomic LC-MS systems (#168)

Rui(Irene) Chen 1 2 , Taiyun Kim 1 2 , Benjamin Parker 2 3 , Sean Humphrey 2 3 , Ben Crossett 4 , Pengyi Yang 1 2 , Jean Yang 1 2
  1. School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
  2. Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
  3. School of Life and Environmental Science, University of Sydney, Sydney, NSW, Australia
  4. Sydney Mass Spectrometry, University of Sydney, Sydney, NSW, Australia

Liquid chromatography-Mass spectrometry (LC-MS) is a mature technology for high-throughput proteomics. The significance of quality control (QC) has been long-acknowledged as a prerequisite for proteomics investigation. Many research laboratories and core facilities implement QC measures as part of their routine workflows. Despite this, few existing QC tools have been developed to assess the performance of the LC-MS systems, and to detect poor or deteriorating performance. Of those that have, often they have specific use cases, are not easily implemented or are not open to public data submission. In addition, different types of instruments have different levels of performance, so platform-dependent QC tests are required.

Here we present a standardized workflow for the rigorous assessment of LC-MS performance. It starts with running of 1 µg HeLa cell tryptic digest, using a defined LC-MS method. Raw data is processed using the MaxQuant computational platform using a consistently-defined method and database.  A series of output files are uploaded to our web-based application to assess the performance of multiple parameters.

The interactive analysis output provides a historical report from the latest runs to as far back as database goes. Advanced options also allow users to interactively compare individual runs, versus those in the database, comparing twelve most important features associated with instrument performance. Unlike previous QC tools, our web-based interactive application does not require any specific set-up, and individual or multiple samples can be analyzed though our application. It also allows users to simultaneously visualize the computational analysis and quantitatively interpret their data while monitoring the performance of their instrument over time by comparing the database. The application will be available to the proteomic community to submit their own samples.