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J Proteome Res. 2016 Dec 2;15(12):4763-4769. Epub 2016 Oct 4.

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

Author information

1
Department of Genome Sciences, University of Washington , Seattle, Washington 98195, United States.
2
LabKey Software , Seattle, Washington 98109, United States.

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 including identification of suboptimal instrument performance, evaluation of ultrahigh pressure chromatography, and identification of the major sources of variation throughout years of peptide data collection.

KEYWORDS:

control charts; process control; proteomics; system suitability; tandem mass spectrometry

PMID:
27700092
PMCID:
PMC5406750
DOI:
10.1021/acs.jproteome.6b00744
[Indexed for MEDLINE]
Free PMC Article

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