MATLAB software for automated calculation of concentration of different compounds using extracted peak area from HPLC data file in pdf format
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Abstract
Chromatograms represent a class of data difficult to process expeditiously due to the large number of intermediary steps necessary to translate peak detection to a concentration reading of a specific compound. This problem is further exacerbated by the different output file format in which instrument manufacturers present chromatographic data. Steps necessary to convert a detected peak to a concentration reading include identification of compound using retention time, extraction of corresponding peak area, and calculation of concentration of compound by using a calibration curve. This work sought to develop a MATLAB software able to automatically extract peak area from chromatographic readout captured in pdf format and calculate the corresponding concentration values. Given manufacturer-specific formatting features in pdf file, the MATLAB software could only read and handle pdf files of HPLC readouts from Shimadzu’s LabSolutions software. In processing the pdf file of each analyzed sample, entire content of the file was first read as a character string. Subsequently, specific delimiters were used to extract retention time and detected peak area for each compound. This information was subsequently processed to identify specific target compound of interest, where extracted peak area was used to calculate concentration of compound using a calibration plot. Overall, the program generates a database comprising filename, raw retention time and peak area data, as well as concentration values of each target compound in an easy to read format. Finally, to provide ease of access and a permanent file for storage, the program output the above database as an Excel file stored on the hard drive. One important advantage of this software is that it could process multiple pdf files simultaneously and there is no upper limit to the number of pdf files (or samples) that could be processed. Collectively, the MATLAB software capable of automatically extracting peak area and calculating concentration of different compounds would provide significant savings of time in handling large number of pdf files in a typical chromatographic run from a Shimadzu HPLC instrument.
Cite this as
2019. MATLAB software for automated calculation of concentration of different compounds using extracted peak area from HPLC data file in pdf format. PeerJ Preprints 7:e27878v2 https://doi.org/10.7287/peerj.preprints.27878v2Author comment
This version corrects a software bug and outlines a software with improved efficiency.
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Additional Information
Competing Interests
The author declares that they have no competing interests.
Author Contributions
Wenfa Ng analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
Software code is available at figshare and can be found from the following link: https://figshare.com/articles/MATLAB_software_for_automatic_reading_of_Shimadzu_HPLC_pdf_files_and_calculating_concentration_of_different_compounds/9121760
Funding
The author received no funding for this work.
