What is NSAF in proteomics?

What is NSAF in proteomics?

Normalized Spectral Abundance Factor (NSAF) for quantitative Liquid Chromatography Mass Spectrometry-Based Proteomics. Normalized spectral abundance factors (NSAFs) provides an improved measure for relative abundance, by factoring the length of the protein into subsequent calculations.

What is label-free mass spec?

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 spectral counting?

Abstract. Spectral count, defined as the total number of spectra identified for a protein, has gained acceptance as a practical, label-free, semiquantitative measure of protein abundance in proteomic studies.

Is MaxQuant free?

MaxQuant is freely available and can be downloaded from this site. 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.

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. Mass spectrometer generated raw files are used for label-free quantitation of proteins.

What is a label-free method?

3.7. 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 label-free sensing?

Label-free technology (also label-free detection or label-free sensing) instead uses impedance- or optics-based biosensors to measure the changes that occur upon analyte binding to a ligand immobilized on a biosensor surface. A defining feature of label-free technology is the method used for ligand immobilization.

Is mass spec quantitative?

Unfortunately, mass spectrometry is not inherently quantitative. Therefore, over the last decade, proteomics researchers have devised a series of stable-isotope labeling strategies to obtain quantitative information.

What is MaxQuant used for?

MaxQuant is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets. It supports all main labeling techniques like SILAC, Di-methyl, TMT and iTRAQ as well as label-free quantification.

Is MaxQuant open source?

MaxQuant is freeware, and contributions to new functionality are collaboration-based. The code of open source parts is available at https://github.com/JurgenCox/compbio-base.

What is an example of NSAF in quantitative proteomics?

Examples of the application of the NSAF approach to quantitative proteomic analysis include work on the expression changes of membrane proteins in S. cerevisiae (Zybailov et al., 2006), on the yeast SIN3/RPD3 complex (Florens et al, 2006), and on the human transcriptional regulatory complex, Mediator (Paoletti et al., 2006).

What is label-free quantitative proteomics?

Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins.

What is the normalized spectral Abundance Factor (NSAF)?

This began with adopting a spectral counting based approach for quantitative proteomics (Zybailov et al., 2005) that led to developing the normalized spectral abundance factor (NSAF) (Zybailov et al., 2006), and most recently distributed NSAF (dNSAF) to deal with peptides shared between multiple proteins (Zhang et al., 2010).

What is the normalized spectral Abundance Factor in quantitative proteomics?

In spectral counting, the total number of tandem mass spectra that match peptides to a particular protein is used to measure the abundance of proteins in a complex mixture. We have developed the normalized spectral abundance factor (NSAF) approach for using spectral counting in quantitative proteomics (Zybailov et al., 2006).