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

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...
Inductively Coupled Plasma Atomic Emission Spectroscopy: Instrumentation01:26

Inductively Coupled Plasma Atomic Emission Spectroscopy: Instrumentation

Inductively coupled plasma (ICP) is the common plasma source used in atomic emission spectroscopy (AES), a technique that detects and analyzes various elements in a sample. This method is often called inductively coupled plasma atomic emission spectroscopy (ICP-AES).
There are three main types of inductively coupled plasma atomic emission spectroscopy  (ICP-AES) instruments: sequential, simultaneous multichannel, and Fourier transform instruments, with the latter being less commonly used.
Atomic Emission Spectroscopy: Overview01:20

Atomic Emission Spectroscopy: Overview

Atomic emission spectroscopy (AES) is an analytical technique used to determine the elemental composition of a sample by analyzing the light emitted from excited atoms. In AES, atoms in a sample are excited to higher energy levels by thermal energy from high-temperature sources, such as plasma, arcs, or sparks. When these excited atoms return to lower energy states, they emit light at specific wavelengths characteristic of each element. The resulting atomic emission spectrum, which consists of...
Mass Analyzers: Overview01:13

Mass Analyzers: Overview

The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
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:
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...

You might also read

Related Articles

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

Sort by
Same author

Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach.

Journal of the American Society for Mass Spectrometry·2026
Same author

From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics.

Journal of proteome research·2025
Same author

Interaction at pre-bonding distances and bond formation for open p-shell atoms with different orientations of their angular momenta.

The Journal of chemical physics·2025
Same author

FastSpel: A Method for Fast Spectral Library Generation.

Journal of proteome research·2025
Same author

Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.

Journal of proteome research·2025
Same author

Biological Function Assignment Across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.

bioRxiv : the preprint server for biology·2025
Same journal

Thymidylate synthase inhibitory drugs induce p53-dependent pathways differently.

PloS one·2026
Same journal

Top-down and bottom-up attention for joint pattern classification and reconstruction.

PloS one·2026
Same journal

Short- and long-term scaling behavior of blood pressure and pulse arrival time during sleep in healthy controls and patients with obstructive sleep apnea.

PloS one·2026
Same journal

Double DQN-based secrecy energy efficiency and fairness performance in IRS-assisted NOMA systems with friendly jamming.

PloS one·2026
Same journal

10 recommendations for strengthening citizen science for improved societal and ecological outcomes: A co-produced analysis of challenges and opportunities in the 21st century.

PloS one·2026
Same journal

Paying in public: Peer effects, impression management, and willingness to pay on digital payment platforms.

PloS one·2026
See all related articles

Related Experiment Video

Updated: Jun 6, 2026

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics.

Gelio Alves1, Aleksey Y Ogurtsov, Yi-Kuo Yu

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.

Plos One
|November 25, 2010
PubMed
Summary
This summary is machine-generated.

A new tool, RAId_aPS, provides spectrum-specific E-values for peptide identification, enabling calibration-free significance assignment and combining results from different search methods for improved accuracy in mass spectrometry data analysis.

More Related Videos

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
14:48

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Published on: May 8, 2021

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain
09:00

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain

Published on: April 28, 2022

Related Experiment Videos

Last Updated: Jun 6, 2026

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
14:48

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Published on: May 8, 2021

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain
09:00

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain

Published on: April 28, 2022

Area of Science:

  • Proteomics
  • Computational Biology
  • Mass Spectrometry

Background:

  • Comparing peptide identification results across different search methods is challenging due to the absence of a universal statistical standard.
  • Previous calibration protocols could lose spectrum-specific statistics and require recalibration for experimental changes.

Purpose of the Study:

  • To develop a novel tool, RAId_aPS, for accurate, calibration-free significance assignment of peptide identification.
  • To enable the combination of results from various search methods using spectrum-specific statistics.

Main Methods:

  • RAId_aPS utilizes dynamic programming to generate score histograms for all possible peptides based on selected scoring functions (RAId score, K-score, Hyperscore, XCorr).
  • The tool assigns E-values using these score histograms, facilitating a calibration-free significance assignment protocol.
  • RAId_aPS offers modes for calculating possible peptides, generating score histograms, reassigning E-values, and performing database searches.

Main Results:

  • RAId_aPS provides spectrum-specific E-values for additive scoring functions.
  • The tool enables calibration-free significance assignment for each scoring function.
  • RAId_aPS can combine results from different scoring functions using spectrum-specific statistics in specific modes.

Conclusions:

  • RAId_aPS offers a robust solution for accurate statistical significance assignment in peptide identification.
  • The tool mitigates issues associated with previous calibration protocols by incorporating spectrum-specific statistics.
  • RAId_aPS facilitates improved comparison and combination of peptide identification results from diverse search methods.