ChromEval: a software application for the rapid evaluation of HPLC system performance in proteomic applications

Area of Science:

• Proteomics
• Analytical Chemistry
• Software Development

Background:

• High performance liquid chromatography (HPLC) is crucial for mass spectrometry-based proteomics, impacting sample identification and reproducibility.
• Effective monitoring of HPLC performance is essential for reliable quantitative analyses, yet tools are limited.
• Existing methods lack comprehensive solutions for rapid HPLC performance assessment in proteomics workflows.

Purpose of the Study:

• To introduce ChromEval, an open-source software application for rapid assessment of HPLC performance in proteomics.
• To provide tools for monitoring mass spectrometer performance, including mass accuracy calibration.
• To enable users to visually assess chromatography quality and troubleshoot issues.

Main Methods:

• Development of an open-source software application, ChromEval.
• Utilizing mzXML files and the Tandem search engine.
• Graphical user interface (GUI) for visualization of superimposed elution peaks of standard peptides.
• Incorporation of quality control runs within regular workflows.

Main Results:

• ChromEval allows visual monitoring of peptide elution, facilitating rapid assessment of chromatography.
• The software identifies chromatography problems like retention time shifts and sample loading variance.
• Provides metrics for mass accuracy calibration and the number of identified peptides from standard mixtures.
• Enables quick, interpretable data generation for go/no-go decisions.

Conclusions:

• ChromEval offers a valuable tool for assessing and troubleshooting HPLC performance in proteomics.
• The software enhances data quality and reproducibility in mass spectrometry-based analyses.
• Facilitates efficient instrument operation and quality control through rapid data interpretation.