Peak-by-Peak

PeakbyPeak is a software tool that automates data processing for breath analysis mass spectrometry. It is optimized for researchers using Super SESI, and produces ready-to-analyze molecular matrices from raw data files.

Breath studies generate large, complex datasets. Aligning files, matching exhalations, grouping isotopes, assigning molecular formulas, and bundling large number of files with large populations requires dedicated advanced coding, data science skills, and years of work.

PeakbyPeak handles everything from file synchronization to molecular annotation with minimal user input. Unlike generic MS tools, it is built for breath analysis and supports Super SESI workflows out of the box.

Developed by Spectroswiss with Fossiliontech to streamline Super SESI analysis workflows.

1. How does Peak-by-Peak eliminate the need for coding or scripting?

It offers a fully graphical and intuitive interface that eases file import, processing, and export. All steps are preconfigured for breath analysis. No coding required.

2. How does Peak-by-Peak align exhalation events with Orbitrap data accurately?

It parses Exhalion logs and matches them with Orbitrap acquisition timestamps to extract the exact spectral frames corresponding to the lung fraction of interest for each exhalation.

3. Why does Peak-by-Peak generate correct spectral calibration automatically?

Abrupt TIC changes transiently distort the MS calibration. Peak-by-Peack applies advanced calibration algorithms to correct and re-calibrate, ensuring accuracy across the full acquisition.

4. How does Peak-by-Peak group isotopic distributions reliably?

It uses advanced deconvolution algorithms to group isotopes, simplifying the spectra and improving the accuracy of Molecular formula assignment.

5. How does Peak-by-Peak assign molecular formulas without expert intervention?

It calculates possible formulas based on accurate m/z, isotope patterns, and adducts. Rulesets are optimized for soft ionization, reducing ambiguity.

6. How does Peak-by-Peak support multi-subject, multi-session, exhalation-by-exhalation studies?

It processes batch datasets, maps files to subjects and sessions, and tracks exhalation-level metadata throughout the pipeline for each recording.

7. How does Peak-by-Peak generate ready-to-analyze molecule × subject × concentration matrices?

It extracts quantitative data for each molecule per exhalation and subject, then compiles structured matrices compatible with statistical tools and machine learning.

8. How does Peak-by-Peak integrate seamlessly with Super SESI and Exhalion workflows?

It was co-developed for real-time SESI-MS and supports native Exhalion metadata, spectral dynamics, and sampling structure out of the box.

9. How does Peak-by-Peak reduce errors in breath data preprocessing?

It handles and automates the process: from file pairing, time alignment, and peak matching, all the way to compiling the full study dataset.

10. How does PeakbyPeak simplify quality control and improve reproducibility in breath analysis?

It logs all processing steps, flags anomalies, and ensures that datasets can be reprocessed identically across time, users, and instruments.