MS File Info Scanner

The MS File Info Scanner can be used to scan a series of MS data files (or data directories) and extract the acquisition start and end times, number of spectra, and the total size of the data, saving the values in the file DatasetTimeFile.txt. It also creates TIC and BPI plots of the data, and can optionally create 2D LCMS plots of m/z vs. time.


Supported file types are:

The software can optionally generate overview plots for visual quality assessment of the data.


Software Instructions

MSFileInfoScanner is a console application. See the Readme on GitHub for details.

Example command line usage:
MSFileInfoScanner.exe QC_Mam_19_01.raw /python /DI /2D /CC /O:QC_Results

Example Results

Category Description Link
Agilent GC/MS QC Plots
Agilent QQQ QC Plots
Agilent AgQTOF QC Plots
Bruker Bruker Xmass BAF 15T QC Plots
DeconTools QC_Shew_15_01 QC Plots
UIMF CCS_PG181Trans_Pos_3 QC Plots
Thermo Angiotensin infusion QC Plots
Thermo Thermo QE HFX QC Plots
Thermo Thermo MRM QC Plots
Thermo Thermo TMT QC Plots
Thermo Thermo with LC device QC Plots
Waters Waters_QTOF QC Plots
Waters Waters_Synapt_HMS QC Plots
Waters Waters_Synapt_IMS QC Plots


All publications that utilize this software should provide appropriate acknowledgement to PNNL and the MS-File-Info-Scanner GitHub repository. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.


These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

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