Jove
Visualize
Contact Us
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 Concept Videos

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...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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...
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 Spectrometers01:16

Mass Spectrometers

This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For example, the mass of helium...

You might also read

Related Articles

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

Sort by
Same author

Site Confidence Scores among All Available Structures to Help Infer Conformational Origins of Identified Cross-Links.

Journal of proteome research·2026
Same author

Deriving wisdom from data: The value and continued rationale for structured data in the era of artificial intelligence-driven oncology care.

Cancer·2026
Same author

Targeting hypersialylation via lectin-directed protein aggregation therapy (LPAT) for anti-metastasis applications.

Biomaterials·2025
Same author

Proteomic study of <i>Akkermansia muciniphila</i> and <i>Bifidobacterium</i> species co-culture under different carbon sources.

Frontiers in microbiology·2025
Same author

Exploring the Potentials of Silver Nanoparticles in Overcoming Cisplatin Resistance in Lung Adenocarcinoma: Insights from Proteomic and Xenograft Mice Studies.

ACS nano·2025
Same author

Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.

Journal of proteome research·2025
Same journal

Identification of Age-Associated Circulating Proteins and Lipids in 3800 Comorbidity-Enriched Older Adults from Japan-Based Cohorts Using Olink Assays and MRM Mass Spectrometry.

Journal of proteome research·2026
Same journal

Molecular Solution to the Paradox of Ancient Brain Preservation.

Journal of proteome research·2026
Same journal

From Method-Defined Signals to Reference Measurement Procedures: Two Decades of Mass Spectrometry-Based ProGRP Quantification.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
Same journal

Hierarchy of MS-Based Evidence.

Journal of proteome research·2026
See all related articles

Related Experiment Video

Updated: Jun 2, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

Lydia Ashleigh Baumgardner1, Avinash Kumar Shanmugam, Henry Lam

  • 1Institute for Systems Biology, Seattle, Washington, USA.

Journal of Proteome Research
|May 7, 2011
PubMed
Summary
This summary is machine-generated.

Mass spectrometry-based proteomics generates large datasets. A new program, FastPaSS, uses graphics processing units (GPUs) to accelerate spectral assignment, overcoming computational bottlenecks in biologic research.

More Related Videos

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)

Published on: March 14, 2013

Related Experiment Videos

Last Updated: Jun 2, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)

Published on: March 14, 2013

Area of Science:

  • Biologic research
  • Proteomics
  • Computational biology

Background:

  • Mass spectrometry-based proteomics is rapidly growing, driven by improved instrumentation.
  • Increasing data output from mass spectrometry instruments creates computational bottlenecks.
  • Spectral assignment, crucial for data analysis, is a rate-limiting step in proteomics.

Purpose of the Study:

  • To address the computational bottleneck in mass spectrometry-based proteomics.
  • To accelerate spectral assignment using graphics processing units (GPUs).
  • To demonstrate the feasibility of GPU computing for spectral assignment in proteomics.

Main Methods:

  • Developed FastPaSS (Fast Parallelized Spectral Searching) program.
  • Implemented FastPaSS using NVIDIA's CUDA for GPU acceleration.
  • Utilized the SpectraST spectral searching algorithm within the CUDA environment.

Main Results:

  • Demonstrated the feasibility of using GPUs for accelerating spectral assignment.
  • FastPaSS effectively distributes and accelerates the spectral assignment process.
  • Proof-of-concept achieved for GPU-accelerated spectral library searching.

Conclusions:

  • GPU computing offers a viable solution to accelerate mass spectrometry data analysis.
  • FastPaSS significantly enhances the efficiency of spectral assignment in proteomics.
  • This approach can alleviate computational bottlenecks in large-scale biologic research.