IDIA

A IDIA tool to generate pseudo-spectra from data independent acquisition (DIA) data mass spectrometry-based proteomics data. The critical innovation of IDIA is that it integrates two isotopic trace detection strategies and employs B-spline and Gaussian filters to help extract high-quality pseudo-spectra from the complex DIA data.

Setup

Dependency

• java version 11
• OpenJDK 11.0.6

Requirement

• 16 GB available RAM or above(based on your data)

User Manual

Download the source code and import them into Eclipse. Export executable Java JAR file. Run JAR file as:

java -jar -Xmx16G IDIA.jar mzMXL_file idia.params

mzXML_file: mzXML format mass spectrum data

idia.params: the parameters of IDIA

Toy example of IDIA

Data Source of the Toy Example

Download the data via the PRIDE repository PXD001587. The UPS2 DIA data files:

18186_REP2_4pmol_UPS2_SWATH_1.wiff

18186_REP2_4pmol_UPS2_SWATH_1.wiff.scan

Converting Raw Data

First step

Download the AB MS Data Converter: https://www.sciex.com/form-pages/sw-downloads-form?d=sciex_ms_data_converter_V1.3.1.zip&asset=software&softwareProduct=MS%20Data%20Converter%201.3.1

The manual of AB MS Data Converter: https://download.sciex.com/sciex-ms-data-converter-user-guide-en.pdf?_ga=2.238304643.2059936003.1661275969-1581161357.1661016015 Command line syntax:

AB_SCIEX_MS_Converter WIFF "18186_REP2_4pmol_UPS2_SWATH_1.wiff" -profile MZML "18186_REP2_4pmol_UPS2_SWATH_1.mzML"

Second step

You convert files from mzML format to mzXML formate by msconvert.exe from ProteoWizard using default parameters. The link of ProteoWizard: https://proteowizard.sourceforge.io/download.html

Run IDIA

Export executable Java JAR file (IDIA.jar) from Eclipse.

Run IDIA as the command line:

java -jar -Xmx16G IDIA.jar 18186_REP2_4pmol_UPS2_SWATH_1.mzXML idia.se_params

The results:

18186_REP2_4pmol_UPS2_SWATH_1_Q1.mgf and 18186_REP2_4pmol_UPS2_SWATH_1_Q2.mgf 18186_REP2_4pmol_UPS2_SWATH_1_Q1.mzML and 18186_REP2_4pmol_UPS2_SWATH_1_Q2.mzML

There are two types of results (mfg and mzML format). Q1 and Q2 are the different quality of the precursor isotopic envelopes.

Peptide and Protein Identification

You can run the database searching engine, Comet, on each pseudo-spectra file followed by PeptideProphet and iProphet to identify peptides. Then you can run ProteinProphet with the results of iProphet to identify proteins. You can apply target-decoy strategy to identify peptides and proteins with 1% FDR.

Feedback

If you have any feedback, please reach out to us at Xuan.Guo@unt.edu and jianchengli@my.unt.edu.