Journey of the mzML Parser & GUI Pipeline

From our first sketches to a working pipeline with an interactive GUI, this page captures the milestones that shaped the project and the visuals that guided each step.

01What We Built

Parsing Pipeline

Extracts MS level 1 spectra from .mzML files and structures the results into JSON for downstream analysis.

Interactive GUI

Guides users through file selection, chemical targeting, and graph generation with a clean PyQt5 interface.

Visualization

Provides quick plots of extracted spectra and offers export-ready views that document the experiment flow.

PyPython + PyQt5 stack
MSMS1 spectra focus
UXGuided, stepwise workflow

Individual Team Roles

  • Austin decoded the binary outputs to keep plotted points accurate and paired with Daniel on GUI polish.
  • Nathanael led stakeholder communication and built the parser that kicked off graph calculations.
  • Emalyn transformed parser numbers into plotted graph files, ensuring calculations reflected correctly.
  • Daniel crafted the upload-friendly GUI so users can generate diverse graphs through SIRIUS.
  • Jason architected the early pipeline research, shaping API, SIRIUS, and MZmine exploration.

02Flowchart Evolution

Initial shorter red flowchart starting from LCMS data collection
Early workflow outlining LCMS intake through initial MZMine tests, parser creation, and first SIRIUS trials.
Current purple flowchart showing the LCMS, MZMine, SIRIUS, and EPA pipeline
Expanded flow linking LCMS collection to MZMine feature finding, SIRIUS predictions, and EPA toxicity review checkpoints.

04Highlights

Data Integrity

MS level 1 filtering ensures we stay focused on the spectra that matter for quick exploratory analysis.

Speed to Insight

The GUI abstracts boilerplate steps—select a file, pick a chemical, view the plot—reducing clicks to insights.

Export-Ready

Graph outputs can be exported for reports, making it easy to share results with collaborators.

05Project Documentation

Background

The Chemical Analysis Instrumentation Lab partnered with PSL to streamline mass spectrometry analysis for water quality research.

Scope & Goals

Deliver a fast, reliable pipeline for MS1 spectra: parse .mzML, visualize KMD calculations, and keep the GUI intuitive.

Known Gaps

Only one chemical compound is currently supported and slope calculations need more validation; x-value ranges still need tuning.

Future Work

Automated moving guide lines on graphs, API integrations with tools like MZmine and SIRIUS, and expanding supported compounds.

UXStep-by-step GUI (Upload → Configure → Visualize)
ReqAutomation, CSV export, tool integration targets
DocsSummarized from the latest team handoff