Label free quantitation

Label free quantitation

Label free quantitation, also referred to as no label quantitation, is based on precursor signal intensity, which is, in most cases applied to data acquired on high mass precision spectrometers equipped with the new generation of time-of-flight (Tof), Fourier transform-ion cyclotron resonance (FTLTQ), or OrbiTrap mass analyzers. The high resolution power facilitates the extraction of peptide signals on the MS1 level and thus uncouples the quantification from the identification process.

The computational framework of label free approach includes detecting peptides, matching the corresponding peptides across multiple LC-MS data, selecting discriminatory peptides.

Detecting Peptides

Typically, peptide signals are detected at the MS1 level and distinguished from chemical noise through their characteristic isotopic pattern. These patterns are then tracked across the retention time dimension and used to reconstruct a chromatographic elution profile of the mono-isotopic peptide mass. The total ion current of the peptide signal is then integrated and used as a quantitative measurement of the original peptide concentration. For each detected peptide, all isotopic peaks are first found and the charge state is then assigned.

Matching Corresponding Peptides

In contrast to differential labelling, every biological specimen needs to be measured separately in a label-free experiment. The extracted peptide signals are then mapped across few or multiple LC-MS measurements using their coordinates on the mass to charge and retention time dimension. Data from high mass precision instruments greatly facilitate this process and increase the certainty of matching correct peptide signals across runs. In addition to the m/z dimension, the TR coordinate is used to map corresponding peptides between runs.

electing Discriminatory Peptides

Finally, sophisticated normalization methods are used to remove systematic artefacts in the peptide intensity values between LC-MS measurements. Then, discriminatory peptides are identified by selecting the peptides whose normalized intensities are different (e.g., p-value < 0.05) among multiple groups of samples.

In addition, newer hybrid mass spectrometers like LTQ OrbiTrap offer the possibility to acquire MS/MS peptide identifications in parallel to the high mass precision measurement of peptides on the MS1 level. This raises the computational challenge for the processing and integration of these two sources of information and has led to the development of novel promising quantification strategies.

References

*cite journal
author=Lukas N. Mueller et al.| date=2008
journal=Journal of Proteome Research
volume=7
pages=51–61
doi=10.1021/pr700758r
title=An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data


Wikimedia Foundation. 2010.

Игры ⚽ Нужно сделать НИР?

Look at other dictionaries:

  • Label-free quantification — is a method in mass spectrometry that aims to determine the differential expression level of proteins in two or more biological samples. Unlike other methods for protein quantification, label free quantification does not use a stable isotope… …   Wikipedia

  • Quantitative proteomics — The aim of quantitative proteomics is to obtain quantitative information about all proteins in a sample. [cite journal |author=Ong SE, Mann M | date=2005 | title=Mass spectrometry based proteomics turns quantitative | journal=Nature Chemical… …   Wikipedia

  • Intact protein expression spectrometry — (IPEx) is a label free quantitation approach in mass spectrometry under development by the analytical chemistry group at the United States Food and Drug Administration Center for Food Safety and Applied Nutrition and elsewhere. Intact proteins… …   Wikipedia

  • Protein mass spectrometry — A mass spectrometer used for high throughput protein analysis. Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important emerging method for the characterization of… …   Wikipedia

  • Cytotoxicity — is the quality of being toxic to cells. Examples of toxic agents are a chemical substance, an immune cell or some types of venom (e.g. from the puff adder or brown recluse spider). Contents 1 Cell physiology 2 Measuring cytotoxicity …   Wikipedia

  • Protein microarray — A protein microarray, sometimes referred to as a protein binding microarray, is a piece of glass on which different molecules of protein have been affixed at separate locations in an ordered manner thus forming a microscopic array. These are used …   Wikipedia

  • The OpenMS Proteomics Pipeline — (TOPP) is a set of computational tools that can be chained together to tailor problem specific analysis pipelines for HPLC MS data. It transforms most of the OpenMS functionality into small command line tools that are the building blocks for more …   Wikipedia

  • Plate reader — Microplate Readers (also known as Plate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality …   Wikipedia

  • Charles Philippe Leblond — Charles Philippe Leblond, Canadian biologist Born February 5, 1910 Lille, France …   Wikipedia

  • Amphetamine — For other uses, see Amphetamine (disambiguation). Amphetamine Systematic (IUPAC) name …   Wikipedia

Share the article and excerpts

Direct link
Do a right-click on the link above
and select “Copy Link”