ISDIA v2.0 - DIA Mass Spectrometry Detection Tool

Cross-platform acquisition-mode detection for mass-spectrometry data. ISDIA provides both command-line and graphical interfaces and supports open formats, Bruker timsTOF data, and vendor formats through ProteoWizard.

Use case	Rapidly distinguish DIA from DDA acquisition patterns
Interfaces	Windows GUI, Windows CLI, Linux CLI
Data formats	mzML, mzXML, Bruker .d / .d.zip, Thermo RAW, SCIEX WIFF
Deployment	Self-contained binaries; no Python installation required
Official release	guomics-lab/ISDIA releases

Overview

ISDIA is a software utility for detecting DIA (Data-Independent Acquisition) mode in mass spectrometry data files.

Development and contribution

ISDIA is developed by Tiannan Guo, Zhiwei Liu, and Wenjie Zhang. For v2.0, Wenjie Zhang contributed to mzML and Bruker timsTOF isolation-window parsing, cross-platform CLI/GUI packaging, and Windows/Linux smoke testing. This repository provides a public distribution and documentation entry point; releases are coordinated through the Guomics Lab repository linked above.

v2.0 New Features:

• ✅ Direct support for Thermo .raw files (via msconvert)
• ✅ Direct support for SCIEX .wiff files (via msconvert)
• ✅ New .mzXML format support (built-in XML parser)
• ✅ Pluggable reader architecture — easy to add more formats
• ✅ Self-contained distribution — copy and run, no Python installation needed

Supported Formats

Format	Extension	Reader	Platform
mzML	.mzML	Built-in XML	Windows / Linux
mzXML	.mzXML, .xml	Built-in XML	Windows / Linux
Bruker timsTOF	.d, .d.zip	Built-in SQLite	Windows / Linux
Thermo RAW	.raw	msconvert (ProteoWizard)	Windows / Linux
SCIEX WIFF	.wiff, .wiff2	msconvert (ProteoWizard)	Windows / Linux

Check format availability:

ISDIA --list-formats

Quick Start

Just Copy and Use! (Windows)

The release package contains both versions — pick whichever you prefer:

1. Download: Get the latest release from GitHub Releases
2. Extract: Unzip to any folder
3. Run:
   • GUI: Double-click ISDIA_gui.exe (graphical interface, recommended)
   • CLI: Open terminal, run ISDIA.exe <input> (command line, suitable for batch processing)
4. Done — no Python, no installation required!

Note: .raw / .wiff / .wiff2 support requires external converter tools. See Converter Setup below to configure them.

If the target computer shows an error about missing msvcp140.dll or vcruntime140.dll, install the Visual C++ Redistributable (most Windows 10/11 machines already have this).

Temporary files: When reading .raw, .wiff, or .wiff2 files, ISDIA temporarily converts them to .mzML format internally. These temporary files are automatically deleted immediately after processing — no cleanup needed, no disk space wasted.

Windows GUI

CLI Usage (Windows Command Line)

# Folder — auto-scan all supported files
ISDIA D:\data\raw_files

# Glob pattern (use quotes around the path!)
ISDIA "D:\data\*.raw"
ISDIA "D:\data\*.d.zip"

# File list (.txt)
ISDIA file_list.txt

# Single file
ISDIA D:\data\sample.raw

# Custom output
ISDIA D:\data --output results.csv

# With custom parameters
ISDIA D:\data --max-ms2 15 --threshold 5

# Disable Pulse DIA detection
ISDIA D:\data --no-pulse-dia

# Specify converter directory (default: ./converters/)
ISDIA D:\data --converter-dir "D:\Program Files\ProteoWizard"

# List supported formats
ISDIA --list-formats

File List Format

Create a text file with one file path per line:

sample001.mzML
sample002.mzXML
sample003.d
sample004.d.zip
sample005.raw
sample006.wiff
sample007.wiff2
D:\data\sample008.raw

Generate file_list.txt from command line:

Windows (PowerShell):

# All supported files in a folder
Get-ChildItem D:\data -Recurse -Include *.mzML,*.mzXML,*.d,*.raw,*.wiff,*.wiff2 | ForEach-Object FullName > file_list.txt

# or using CMD
dir /b /s D:\data\*.mzML D:\data\*.raw > file_list.txt

Linux:

# All supported files in a folder
find /d/west -type f \( -name "*.mzML" -o -name "*.mzXML" -o -name "*.raw" -o -name "*.wiff" -o -name "*.wiff2" \) > file_list.txt

# timsTOF .d folders
find /d/west -type d -name "*.d" > file_list.txt

Tip: In most cases you don't need to create file_list.txt manually. Just pass the folder path directly — ISDIA scans it automatically.

Output Format

CSV file with columns:

• FileName: Input file name
• FileExists: Whether the file was found
• MS2Count: Number of MS2 scans detected
• MS2isoContinue: Number of consecutive isolation windows
• ISDIA: DIA detection result (Yes / No / Unknown)
• Format: File format detected

Algorithm Details

ISDIA determines DIA mode by analyzing the isolation window patterns of MS2 scans:

1. MS2 Scan Collection: Extract the first N MS2 scans from the file
2. Isolation Window Extraction: Get target m/z, lower offset, upper offset
3. Continuity Check: Check if consecutive windows satisfy:
   • targetMZ(i) + 1 <= targetMZ(i+1)
   • iso_upper(i) + tolerance >= iso_lower(i+1)
4. Classification: >= 3 consecutive windows → DIA; otherwise → DDA
5. Pulse DIA (optional): Check for periodic window patterns with 3 equal m/z differences

Converter Setup for .raw / .wiff

Windows: Install ProteoWizard, then copy all files in the installation directory (including msconvert.exe, vendor DLLs and other dependencies) to converters/msconvert/. Alternatively, use --converter-dir to point to the ProteoWizard installation path directly.

Linux (cluster without sudo):

Step 1 — install a container runtime (ask your admin, or install yourself via conda):

# Apptainer (Singularity successor) via conda
conda install -c conda-forge apptainer -y

# or the classic SingularityCE
conda install -c conda-forge singularityce -y

# verify
which apptainer || which singularity

Note: If neither is available, alternatives are (a) conda install -c conda-forge wine to run msconvert.exe under Wine, or (b) pre-convert .raw/.wiff to .mzML on a Windows machine.

Step 2 — build the ProteoWizard Singularity container from Docker Hub:

singularity pull pwiz.sif docker://proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses

• This downloads pwiz.sif (~2 GB). Place it in converters/msconvert/. ISDIA auto-detects it — no --msconvert-container flag needed. (Explicit flag still works and takes priority.)

Linux Usage

The Linux binary is self-contained (no Python/pip required).

# Make executable
chmod +x ISDIA

# Folder — auto-scan all supported files
./ISDIA /data/raw_files

# Glob pattern (use quotes!)
./ISDIA "/data/*.raw"
./ISDIA "/data/*.d.zip"

# File list (.txt)
./ISDIA file_list.txt

# Custom output and parameters
./ISDIA /data/raw_files --output results.csv --max-ms2 15 --threshold 5

# Disable Pulse DIA detection
./ISDIA /data/raw_files --no-pulse-dia

# With Singularity container (cluster without sudo) — auto-detected from converters/
./ISDIA /data/raw_files

# Explicit container path (optional, overrides auto-detection)
./ISDIA --msconvert-container ./converters/msconvert/pwiz.sif /data/raw_files

# List supported formats
./ISDIA --list-formats

Performance

Operation	Speed
.mzML parsing	~1-2s / file (depends on file size)
.d (timsTOF)	~0.1s / file (SQLite query)
.raw (msconvert, progressive)	~2-10s / file (first 50 scans)
.wiff (msconvert, progressive)	~2-10s / file (first 50 scans)

Troubleshooting

"Converter not found" error

Use --list-formats to check converter status. Install missing tools as described above.

Missing DLL error (msvcp140.dll / vcruntime140.dll)

Install Visual C++ Redistributable. Most Windows 10/11 systems already include these.

.raw file reads slowly

ISDIA uses progressive scan range (50→500→5000→50000). If all limits are reached, the file may have very few MS2 scans.

.raw / .wiff on Linux

Options:

1. Container (recommended) — install Apptainer/Singularity (conda install -c conda-forge apptainer), download the .sif file, use --msconvert-container. No sudo required.
2. Wine — sudo apt install wine (or conda install -c conda-forge wine), then copy msconvert.exe and vendor DLLs from a Windows ProteoWizard installation into converters/msconvert/.

Or pre-convert on a Windows machine.

Temporary files filling disk

No need to worry — all temporary .mzML files from .raw/.wiff/.wiff2 conversion are automatically deleted by ISDIA immediately after processing. If a crash occurs mid-conversion, leftover temp files can be found in the system temp directory (usually %TEMP%) under names starting with isdia_ — you can safely delete them manually.

Parameters

Parameter	Default	Description
--output, -o	isdia_results.csv	Output CSV file path.
--max-ms2	11	Maximum number of MS2 scans to extract. The default is an empirical value sufficient for acquisition mode judgment; larger values increase processing time.
--threshold	3	Number of consecutive isolation windows required to classify as DIA. Increase to reduce false positives.
--tolerance	0.1	m/z tolerance for comparing adjacent isolation window boundaries. Larger values are more permissive.
--pulse-dia	on	Pulse DIA detection mode. Runs automatically as a secondary check; has no effect on standard DIA detection.
--no-pulse-dia	—	Disable Pulse DIA detection.
--pulse-tol	0.01	Tolerance for detecting equal m/z differences in Pulse DIA mode. Smaller values require stricter periodicity.
--converter-dir	./converters/	Path to msconvert.exe and vendor DLLs (Windows).
--msconvert-container	—	Path to Singularity .sif container with Wine + msconvert (Linux clusters).
--list-formats	—	Display all supported file formats and converter availability.

Parameter Guidance

• DDA vs DIA discrimination: Default parameters (--max-ms2 11 --threshold 3 --tolerance 0.1) work well for most datasets. If false positives occur, increase --threshold or decrease --tolerance.
• Pulse DIA: Enabled by default. Pulse DIA check only activates when standard detection fails, acting as a safety net with no impact on normal DIA detection. Disable with --no-pulse-dia if needed.

Terms of Use

This software is provided for academic research use only. Redistribution must include all original files including the converters/ directory. The software is protected by Chinese software copyright (Registration No. 2026SR0602039).

Citation

Tiannan Guo, Zhiwei Liu, Wenjie Zhang. ISDIA software [Z]. 2026SR0602039. 2026.

Contact

• Email: liuzhiwei@westlake.edu.cn
• Issues: GitHub Issues

For commercial cooperation, please contact us.