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Peptide Identification Using Tandem Mass Spectrometry

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...

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Related Experiment Video

Updated: Oct 22, 2025

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

Published on: June 4, 2021

The utilization of the search engine, Bolt, to decrease search time and increase peptide identifications in hydroxyl

Emily E Chea¹, Amol Prakash², Lisa M Jones¹

¹Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland, USA.

|August 31, 2021

Summary

This summary is machine-generated.

Hydroxyl radical protein footprinting (HRPF) identifies protein structural changes. A new cloud-based engine, Bolt, identified 35% more modified peptides than Sequest, significantly reducing computation time.

Keywords:

Bolt Pinnacle Sequest hydroxyl radical protein footprinting (HRPF)proteomics

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Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes

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Published on: September 1, 2020

Area of Science:

Proteomics
Biochemistry
Structural Biology

Background:

Hydroxyl radical protein footprinting (HRPF) analyzes protein structures by detecting modifications on solvent-exposed regions.
Mass spectrometry coupled with HRPF provides insights into protein structural dynamics within cellular environments.
Identifying HRPF modifications is computationally intensive, often requiring days for proteome-wide analysis.

Purpose of the Study:

To evaluate the efficiency of a novel cloud-based search engine, Bolt, for identifying HRPF modifications.
To compare the performance of Bolt against a conventional search engine, Sequest, in terms of identification rates and processing time.

Main Methods:

Utilized hydroxyl radical protein footprinting (HRPF) to label proteins.
Employed mass spectrometry for peptide analysis.
Compared the performance of the Bolt cloud-based search engine with the Sequest search engine for HRPF data analysis.

Main Results:

Bolt demonstrated a 35% increase in the identification of modified peptides compared to Sequest.
Bolt significantly decreased the computational time required for searching HRPF modifications.
The study confirmed Bolt's capability to handle complex proteomic datasets with HRPF modifications.

Conclusions:

The Bolt cloud-based search engine offers a substantial improvement in identifying HRPF modifications.
Bolt provides a faster and more comprehensive approach to analyzing protein structural changes using HRPF.
This advancement in computational analysis facilitates deeper insights into protein structure and function.