An Automated Pipeline to Monitor System Performance in Liquid Chromatography–Tandem Mass Spectrometry Proteomic Experiments

Abstract

We report the development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments. LC MS/MS runs are automatically imported into Skyline and multiple identification free metrics are extracted from targeted peptides. These data are then uploaded to the Panorama Skyline document repository where metrics can be viewed in a web based interface using powerful process control techniques, including Levey-Jennings and Pareto plots. The interface is versatile and takes user input which allows the user significant control over the visualization of the data. The pipeline is vendor and instrument type neutral, supports multiple acquisition techniques (e.g. MS 1 filtering, data independent acquisition, parallel reaction monitoring, and selected reaction monitoring), can track performance of multiple instruments, and requires no manual intervention aside from initial setup. Data can be viewed from any computer with internet access and a web browser -- facilitating sharing of QC data between researchers. Herein we describe the use of this pipeline, termed Panorama AutoQC, to evaluate LC MS/MS performance in a range of scenarios from identification of suboptimal instrument performance, evaluation of ultra-high pressure chromatography, to the identification of the major sources of variation throughout years of peptide data collection.

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

“…Sophisticated QC tools have been published and already found extensive applications in the field, such as Statistical Process Control in Proteomics (SProCoP) [56], that can be installed as external tool in Skyline; or Panorama AutoQC [57], which can automatically import raw data and system performance of any targeted (SRM/PRM) or uDIA.…”

“…Much more robust system operation including automatic quality control (Panorama AutoQC) [57] and more stable electrospray, for example, by switching from nano-flow to micro-flow HPLC [86], will provide sufficient reliability for the typical day-today use. Altogether, continued improvements to reliability and usability of uDIA workflows will open numerous possibilities for clinical and pre-clinical studies.…”

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

“…Storing Skyline documents in Panorama does not confer any loss of information and data can be made public or kept private at the discretion of the researcher.It is possible to automate entire informatics pipelines, from acquisition to Panorama publishing, using the command-line version of Skyline, called SkylineRunner. An exemplary case of informatics automation is AutoQC, a completely automated pipeline designed to monitor system suitability in bottom-up proteomics 81. As a mass spectrometer runs, AutoQC imports quality control acquisitions into Skyline, extracts multiple identification-free metrics, and uploads the data to a Panorama Skyline document repository.…”

Updates on resources, software tools, and databases for plant proteomics in 2016–2017

“…Panorama AutoQC is a tool that evaluates LC–MS/MS performance in conditions such as identification of suboptimal instrument runs, quality control for ultrahigh pressure chromatography, and in the identification of the major sources of unwanted variation through several years of proteomics collection .…”