Related Experiment Video
Updated: Dec 30, 2025
07:01
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
700
Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
Bart Van Puyvelde1, Sander Willems1, Ralf Gabriels2,3
1ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Ghent, Belgium.
Proteomics
|January 26, 2020
Summary
Data-independent acquisition (DIA) now offers deep peptide detection without data-dependent acquisition (DDA) libraries. Combining predicted intensities and retention times with narrow window DIA makes the workflow deterministic and improves clinical proteomics comparisons.
Area of Science:
- Proteomics
- Mass Spectrometry
- Analytical Chemistry
Background:
- Data-independent acquisition (DIA) in mass spectrometry generates complex data.
- Deep peptide detection typically requires data-dependent acquisition (DDA) libraries.
- Current DIA workflows can have variations and stochastic sampling issues.
Purpose of the Study:
- To eliminate the dependency on DDA libraries for DIA.
- To develop a deterministic DIA workflow for enhanced peptide detection.
- To facilitate inter-laboratory comparisons in clinical proteomics.
Main Methods:
- Combining predicted fragment intensities with retention times.
- Implementing narrow window DIA acquisition.
- Developing a library-free DIA approach.
Main Results:
- Achieved deep peptide-centric detection in DIA without DDA libraries.
- Demonstrated a fully deterministic DIA workflow.
- Eliminated variation associated with library building and stochastic sampling.
Conclusions:
- DIA can be performed without DDA libraries by integrating predicted data.
- The novel DIA approach enhances reproducibility and comparability, particularly for clinical applications.
- This advancement simplifies and standardizes proteomic data analysis.
Related Concept Videos
01:20¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)
1.5K
When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
1.5K
01:04¹³C NMR: ¹H–¹³C Decoupling
1.6K
The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
1.6K
01:16IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration
2.6K
A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to...
According to Hooke's law, the vibrational frequency is directly proportional to...
2.6K
01:24Mass Spectrum: Interpretation
2.5K
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...
2.5K
01:32UV–Vis Spectroscopy of Conjugated Systems
8.1K
Organic compounds with conjugated double bonds show strong absorption features in the UV–visible region of the electromagnetic spectrum attributed to π → π* electronic excitations. Generally, a UV–vis absorption spectrum is recorded as a plot of absorbance vs wavelength. The wavelength of maximum absorbance, which manifests as a peak in the absorption spectrum, is denoted as λmax.
One of the factors influencing λmax is the extent of conjugation in...
One of the factors influencing λmax is the extent of conjugation in...
8.1K
01:25Atomic Absorption Spectroscopy: Interference
1.9K
Interference leads to systematic error in atomic absorption (AA) measurements by enhancing or diminishing the analytical signal or the background. These interferences can be grouped into three main categories: spectral interference, chemical interference, and physical interference.
Spectral interference occurs when signals from other elements or molecules overlap with the analyte signal, falsely elevating or masking the analyte's absorbance. This interference can be corrected using Zeeman,...
Spectral interference occurs when signals from other elements or molecules overlap with the analyte signal, falsely elevating or masking the analyte's absorbance. This interference can be corrected using Zeeman,...
1.9K