Label-free protein quantification is a mass spectrometry-based method for identifying and quantifying relative changes in two or more biological samples instead of using a stable isotope-containing compound to label proteins.

What is a label-free quantitative mass spectrometry?

Label-free protein quantification is a mass spectrometry-based method for identifying and quantifying relative changes in two or more biological samples instead of using a stable isotope-containing compound to label proteins.

How does label-free quantification work?

Label-free quantification is a method in MS that determines the relative amount of proteins in two or more biological samples, but unlike other quantitative methods, is does not use a stable isotope that chemically binds and labels the protein.

What is Lfq intensity?

LFQ (label-free quantitation) intensity is a very similar to the iBAQ intensity but the protein intensities are normalized to exculde some “outliers” to best represent the ratio changes of different samples.

What is label-free imaging?

What is label-free imaging? Label-free imaging, as the name suggests, can be defined as a method for visualizing cells that have not been labeled or altered in any way. To achieve this goal brightfield, phase contrast, and differential interference contrast microscopy can be used to visualize label-free cells.

How is iBAQ value calculated?

We used MaxQuant to calculate iBAQ, a measure of protein abundance. The iBAQ value is obtained by dividing protein intensities by the number of theoretically observable tryptic peptides between 6 and 30 amino acids29, and is on average highly correlated with protein abundance29,39.

Why is label-free detection important?

In a typical biosensing process, molecular interactions are transduced as mechanical, electrical, or optical signals, and are thus detectable without any label probes. The main advantage for label-free detection is that more direct information can be acquired, as the methods use only native proteins and ligands.

What is label-free cell?

Label-free cell analysis is essential to personalized genomics, cancer diagnostics, and drug development as it avoids adverse effects of staining reagents on cellular viability and cell signaling.

What is label-free microscopy?

Label-free imaging, as the name suggests, can be defined as a method for visualizing cells that have not been labeled or altered in any way. To achieve this goal brightfield, phase contrast, and differential interference contrast microscopy can be used to visualize label-free cells.

What is the name of the search engine that MaxQuant has?

The download includes the search engine andromeda, which is integrated into MaxQuant as well as the viewer application for inspection of raw data and identification and quantification results. For statistical analysis of MaxQuant output, we offer the Perseus framework.

What is label-free quantitative proteomics?

Label-free quantitative proteomics approach provides a powerful tool to resolve and identify thousands of proteins from a complex biological sample. In this approach, proteins are first digested with a protease into a peptide mixture, which is subsequently analyzed by tandem MS (MS/MS) and identified by database searching.

What are the steps in label-free protein quantification?

Creative Proteomics’ label-free quantification services consist of the following four fundamental steps: Sample preparation – protein extraction, reduction, alkylation and digestion; Data analysis – identification, quantification and statistical analysis; Figure 1. A typical workflow chart for LC/MS-based label-free protein quantification.

What is label-free quantification in LC-MS?

MS-based label-free quantification aims to directly compare relative abundances of proteins across multiple LC-MS/MS experiments without utilizing stable isotopes or isotopic tags. There are two commonly used quantitative schemes: (1) mass spectral peak intensities and (2) spectral counting.

What is the label-free approach to peptide profiling?

In principle, the label-free approach is based on peptide intensity profiling. The relative abundance of a specific modified peptide is obtained by integrating the area under its peak and then dividing it by the sum area of that peptide in unmodified and all modified forms.