PEAKS Quantification: ICAT, iTRAQ, Label Free, SILAC, User Defined Labeling

After proteins have been identified, PEAKS Q (an optional node) identifies abundance ratios from a variety of quantification methods including:

As proteomic quantification is an emerging application, many researchers may not yet know a great deal about which quantification methods offer advantages that others do not, and vice versa. Therefore, we have created a very short overview of quantification and it is available for download here: Basics of quantification.pdf

While many quantification methods require different algorithms, some issues are able to be treated uniformly, such as removal of outlines and visualization. To read more about abundance ratios, please click here.

Visual inspection of raw spectra becomes very important. It allows researchers the chance to adjust the parameter setting to gain much more accurate ratios. The PEAKS quantification package provides a 2D view of the MS/MS spectrum as well as a 3D view of the parent scan for each identified peptide. Thus the actual ratios can be easily verified by inspecting the correspondent raw spectra.

Isobaric tagging for relative and absolute quantification (iTRAQ) uses isotopic labeling to enable relative quantification comparisons. Up to eight different proteomic samples can be labeled using eight different isobaric tags.
ITRAQ Poster

Label Free quantification relies on the changes in analyte signals directly reflecting their concentrations in one sample relative to another. This technology employs overall spectral intensity normalization by interpreting signals of molecules that do not change concentration from sample to sample. By comparing two or more spectra, PEAKS can determine the constant intensity ratio between the unchanging analytes forms the basis for identifying the non-changing concentrations, making spiking unnecessary.
Label Free Poster

Stable isotope labeling with amino acids in cell culture (SILAC) is a method to metabolically label proteins for relative quantification comparison. One cell population is fed amino acids of normal isotopic composition; the other cell population is fed amino acids labeled with heavier isotopes. The heavy amino acids are incorporated into newly synthesized proteins, eventually completely replacing the cells� proteins, such that labeling efficiency is near 100%. The cell populations are then mixed together and digested for MS analysis to determine differential protein abundances.

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Overview De Novo Sequencing Database Search Multiple Database Search Sequence Homology PTM Quantification RAW Data Tech Support Our Research User Comments User Research Download Demo Request Prices	Superior de novo sequencing and protein ID Software PEAKS PEAKS Quantification (PEAKS Q) After proteins have been identified, PEAKS Q (an optional node) identifies abundance ratios from a variety of quantification methods including: ICAT (Isotope Coded Affinity Tags) ICPL (Isotope Coded Protein Labels) Flexible Labeling iTRAQ (Isobaric Tag for Relative and Absolute Quantification) Label Free Quantification N-Terminal Labeling SILAC (Stable Isotope Labeling with Amino Acids in Cell Culture) TMT (Tandem Mass Tags) User Defined Labeling As proteomic quantification is an emerging application, many researchers may not yet know a great deal about which quantification methods offer advantages that others do not, and vice versa. Therefore, we have created a very short overview of quantification and it is available for download here: Basics of quantification.pdf Abundance Ratios While many quantification methods require different algorithms, some issues are able to be treated uniformly, such as removal of outlines and visualization. To read more about abundance ratios, please click here. Visual Inspection Visual inspection of raw spectra becomes very important. It allows researchers the chance to adjust the parameter setting to gain much more accurate ratios. The PEAKS quantification package provides a 2D view of the MS/MS spectrum as well as a 3D view of the parent scan for each identified peptide. Thus the actual ratios can be easily verified by inspecting the correspondent raw spectra. iTRAQ Quantification Isobaric tagging for relative and absolute quantification (iTRAQ) uses isotopic labeling to enable relative quantification comparisons. Up to eight different proteomic samples can be labeled using eight different isobaric tags. ITRAQ Poster Label Free Qauntification Label Free quantification relies on the changes in analyte signals directly reflecting their concentrations in one sample relative to another. This technology employs overall spectral intensity normalization by interpreting signals of molecules that do not change concentration from sample to sample. By comparing two or more spectra, PEAKS can determine the constant intensity ratio between the unchanging analytes forms the basis for identifying the non-changing concentrations, making spiking unnecessary. Label Free Poster SILAC Quantification Stable isotope labeling with amino acids in cell culture (SILAC) is a method to metabolically label proteins for relative quantification comparison. One cell population is fed amino acids of normal isotopic composition; the other cell population is fed amino acids labeled with heavier isotopes. The heavy amino acids are incorporated into newly synthesized proteins, eventually completely replacing the cells� proteins, such that labeling efficiency is near 100%. The cell populations are then mixed together and digested for MS analysis to determine differential protein abundances.