Unassigned MS/MS Spectra: Who Am I?
Mohashin Pathan1, Monisha Samuel2, Shivakumar Keerthikumar1
1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
Methods in Molecular Biology (Clifton, N.J.)
|December 16, 2016
Summary
High-quality mass spectrometry (MS) data requires advanced bioinformatics tools for protein identification. This work discusses methods to analyze unassigned tandem MS spectra, improving protein discovery.
Area of Science:
- Proteomics
- Bioinformatics
- Analytical Chemistry
Background:
- High-resolution tandem mass spectrometry (MS) generates high-quality data.
- Bioinformatics software has advanced for analyzing MS datasets.
- Despite advances, protein identification from MS data remains challenging.
Purpose of the Study:
- To discuss tools for protein identification using mass spectrometry.
- To explore methods for assigning unassigned tandem MS spectra.
- To address challenges in MS data analysis.
Main Methods:
- Review of bioinformatics tools for protein identification.
- Analysis of factors contributing to unassigned MS/MS spectra.
- Discussion of strategies for spectral assignment.
Main Results:
- Approximately 60% of MS/MS spectra remain unassigned in typical analyses.
- Unassigned spectra can result from low quality, search space limitations, annotation errors, or posttranslational modifications.
- High-quality unassigned spectra warrant further investigation.
Conclusions:
- Effective protein identification relies on robust MS data analysis.
- Assigning unassigned tandem MS spectra is crucial for comprehensive proteomic studies.
- Further research can elucidate the causes of unassigned spectra to enhance protein discovery.
Related Concept Videos
01:21Tandem Mass Spectrometry
2.8K
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...
2.8K
01:23Mass Spectrum
5.2K
A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
5.2K
01:24Mass Spectrum: Interpretation
3.7K
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...
3.7K
01:16Mass Spectrometers
9.7K
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:
9.7K
01:19MALDI-TOF Mass Spectrometry
7.3K
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...
7.3K
01:15High-Resolution Mass Spectrometry (HRMS)
2.8K
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...
2.8K