Jove
Visualize
Contact Us

Related Concept Videos

MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

6.3K
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...
6.3K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

2.1K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
2.1K
Discrete-Time Fourier Series01:20

Discrete-Time Fourier Series

570
The Discrete-Time Fourier Series (DTFS) is a fundamental concept in signal processing, serving as the discrete-time counterpart to the continuous-time Fourier series. It allows for the representation and analysis of discrete-time periodic signals in terms of their frequency components. Unlike its continuous counterpart, which utilizes integrals, the calculation of DTFS expansion coefficients involves summations due to the discrete nature of the signal.
For a discrete-time periodic signal x[n]...
570
Relation of DFT to z-Transform01:20

Relation of DFT to z-Transform

701
The Discrete Fourier Transform (DFT) is a crucial tool for analyzing the frequency content of discrete-time signals. It converts a sequence of N samples from the time domain into its corresponding sequence in the frequency domain, where each sample represents a specific frequency component.
To understand how the DFT works, it's helpful to consider the z-transform, which is a method for representing discrete sequences in the complex frequency domain. The z-transform involves summing the...
701
Fast Fourier Transform01:10

Fast Fourier Transform

765
The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log⁡2N multiplications, offering a much faster performance.
The computational efficiency of the FFT becomes...
765
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C 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

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE).

Bioinformatics (Oxford, England)·2021
Same author

Strategies to enable large-scale proteomics for reproducible research.

Nature communications·2020
Same author

Addressing the Challenges of High-Throughput Cancer Tissue Proteomics for Clinical Application: ProCan.

Proteomics·2019
Same author

A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs.

Journal of proteome research·2019
Same author

Subject-specific multi-poroelastic model for exploring the risk factors associated with the early stages of Alzheimer's disease.

Interface focus·2017
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Dec 19, 2025

Author Spotlight: Quantification of Complex Lipidomic Samples Using Stable Isotope Labeling
07:12

Author Spotlight: Quantification of Complex Lipidomic Samples Using Stable Isotope Labeling

Published on: August 23, 2024

1.7K

Toffee - a highly efficient, lossless file format for DIA-MS.

Brett Tully1

  • 1The ACRF International Centre for the Proteome of Human Cancer (ProCan), Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia. brett.tully@magd.oxon.org.

Scientific Reports
|June 4, 2020
PubMed
Summary
This summary is machine-generated.

A new open data format, toffee, addresses mass spectrometry challenges. It offers smaller file sizes and faster data access than mzML, enabling advanced bioinformatics and deep learning for proteomics.

More Related Videos

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
09:38

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Published on: November 26, 2013

14.5K
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

643

Related Experiment Videos

Last Updated: Dec 19, 2025

Author Spotlight: Quantification of Complex Lipidomic Samples Using Stable Isotope Labeling
07:12

Author Spotlight: Quantification of Complex Lipidomic Samples Using Stable Isotope Labeling

Published on: August 23, 2024

1.7K
Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
09:38

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Published on: November 26, 2013

14.5K
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

643

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Vendor-specific file formats in mass spectrometry hinder bioinformatics software development.
  • The open mzML format, while adopted, faces challenges with large file sizes and sequential I/O, especially in high-throughput proteomics.
  • Efficient data handling is crucial for advancing mass spectrometry data analysis.

Purpose of the Study:

  • Introduce 'toffee', an open, random I/O data format for mass spectrometry data.
  • Address the limitations of the mzML format regarding file size and data access.
  • Enable novel applications in proteomics data analysis through improved data access patterns.

Main Methods:

  • Developed 'toffee' as an open format utilizing HDF5 for random I/O.
  • Implemented lossless compression to achieve file sizes comparable to vendor formats.
  • Demonstrated reconversion from 'toffee' to mzML without data loss.
  • Evaluated 'toffee' performance using OpenSWATH algorithms.

Main Results:

  • 'toffee' achieves file sizes similar to original vendor formats with lossless compression.
  • Random I/O access patterns are enabled, overcoming mzML's sequential limitations.
  • Equivalence in data processing with OpenSWATH algorithms was demonstrated between mzML and 'toffee'.
  • A peptide-centric deep-learning pipeline for peptide identification was proposed, enabled by 'toffee's access patterns.

Conclusions:

  • 'toffee' provides an efficient, open data format for mass spectrometry, overcoming mzML limitations.
  • The format facilitates high-throughput proteomics and enables new computational approaches, such as deep learning for peptide identification.
  • Availability of documentation and open-source code promotes community adoption and further development.