SDF2PQI (SDF to PQI Library Converter)

In production.

Progenesis QI and Structure-Data files (SDF) incompatibility

Progenesis™ QI v2.4 (PQI, Waters Corporation™ © Nonlinear Dynamics) is a bioinformatic/chemometric tool that processes raw data from high-resolution Mass Spectrometry (MS). It facilitates the identification workflow for Metabolomics experiments using molecule libraries with Precursor's structure (structure-data file, .sdf) and its Fragments (main spectra profile, .msp) for features annotation (identification).

PQI has several ways to search for molecule matches, using mainly internal molecule libraries but also, not officially, external libraries. The main spectra repository available are The Human Metabolome Database (HMDB), Lipid Maps and MassBank of North America (MoNA), which considerably increases the number and quality of metabole identification.

Due to its non-official nature, a lot of problems have been shown, the main reason being the differences in the formatting of external .sdf file and internal .sdf files used by PQI. Also, this formatting problem causes failure in the crosstalk between .sdf and .msp files, essential to relate the Precursor Ion with its Fragments for identifying unknown metabolites.

Solution

We developed a console application, names SDF2PQI (SDF to PQI Library Converter) to solve these formatting problems, enabling compatibility among SDF libraries and PQI and making them readily available to increase PQI's capabilities.

Instructions

1. Go to the SDF download page (HMDB; Lipid Maps; MoNA) and download the "SDF" (structure-data file). It will be downloaded as a .zip file, corresponding to the library you prefered.
2. Extract the .zip file.
3. Inside de SDF to PQI Converter Folder, open the .sdf file and save it as "input.txt".
4. Click on the "sdf_to_pqi.exe" executable (.exe) file.
5. A command prompt will show up. Don't close it. The file's lines will be scanned and corrected. Wait until the conversion process is done.
6. Converted files will be generated as "output.sdf" and "output.msp".
7. They are read to be used in Progenesis QI Metascope identification search.
8. Every time a library will ber converted, should be only one input.txt file inside the folder. We recommend you move the output files from there.

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Citation: Sanches et al., Fitting Structure-Data Files (.SDF) Libraries to Progenesis QI Identification Searches. J. Braz. Chem. Soc. 2023.

DOI: 10.21577/0103-5053.20230016.

Main Authors: Pedro H. Godoy Sanches, Ivan G. M. dos Reis and Gustavo H. B. Duarte.