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Related Concept Videos

MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Matrix-Assisted Laser Desorption Ionization (MALDI)01:08

Matrix-Assisted Laser Desorption Ionization (MALDI)

Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and characterization of various biomolecules, including proteins, peptides, nucleic acids, and carbohydrates. MALDI is an ionization technique, widely employed in biological and medical research, as well as in fields like pharmacology and biochemistry.The analyte of interest, a biomolecule or a mixture of biomolecules, is mixed with a suitable matrix...

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Related Experiment Video

Updated: May 18, 2026

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow
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Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Published on: April 18, 2019

MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures.

Lochana C Menikarachchi1, Shannon Cawley, Dennis W Hill

  • 1Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Road, Storrs, Connecticut 06269, United States.

Analytical Chemistry
|October 9, 2012
PubMed
Summary

MolFind software aids chemical structure identification in complex mixtures using HPLC/MS data. It filters candidate compounds from databases, improving identification accuracy in metabolomics research.

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Last Updated: May 18, 2026

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Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Biochemistry

Background:

  • Metabolomics studies require accurate identification of chemical structures in complex biofluids.
  • High-performance liquid chromatography/mass spectrometry (HPLC/MS) is a key technology for analyzing these mixtures.
  • Current methods for structure identification can be limited by the complexity of the data and the size of chemical databases.

Purpose of the Study:

  • To present MolFind, a multithreaded software package designed to aid in identifying chemical structures from HPLC/MS data.
  • To improve the efficiency and accuracy of compound identification in metabolomics.
  • To enable matching experimental HPLC/MS data with computationally derived values from chemical databases.

Main Methods:

  • MolFind utilizes a pipeline approach for processing HPLC/MS data.
  • It filters candidate compounds from databases (e.g., PubChem) based on monoisotopic molecular weight.
  • Computational predictions of retention index (RI), ECOM(50), drift time, and collision-induced dissociation (CID) spectra are used for filtering and ranking.

Main Results:

  • Current RI and ECOM(50) models filter approximately 28% of compounds from database bins.
  • Quantitative structure-property relationship (QSPR) modeling of drift times showed improved correlation with experimental data.
  • Filtering with RI and ECOM(50) models improved the ranking of unknown compounds in 23 of 35 cases, with the correct compound ranked in the top 20 in 19 cases.

Conclusions:

  • MolFind enhances the identification of chemical structures in complex mixtures by integrating multiple predictive models.
  • The software shows significant potential for improving the accuracy and efficiency of metabolomics research.
  • Further inclusion of chemical structures in computational models could increase filtering efficiency to up to 87%.