I performed analysis of my proteomics data in MaxQuant to compare different samples together; I get excel sheet from protein group I would like to know what is the difference between plain intensity and LFQ intensity?
From the paper about iBAQ (https://www.nature.com/articles/nature10098), MaxQuant computes protein intensities as the sum of all identified peptide intensities (maximum detector peak intensities of the peptide elution profile, including all peaks in the isotope cluster). Protein intensities were divided by the number of theoretically observable peptides (calculated by in silico protein digestion with a PERL script, all fully tryptic peptides between 6 and 30 amino acids were counted while missed cleavages were negelected).
Yes, Ilian Atanassov is right. iBAQ is the total intensities divided by the identified peptides for one protein.
It is hard to do absolute quantification of proteins. iBAQ works if all peptides were ionized and detected at the same efficency.
LFQ is very similar to the "protein intensities" used by iBAQ. It is normalized to exculde some "outliers" to best represent the ratio changes of different samples.
I think since the MaxQuant program can report intensity, LFQ and iBAQ, iBAQ can be used to compare the "molar" amount of different proteins, LFQ for comparison between samples, and intensity for some complex cases (e.g. some fractions were diluted or treated differently).
I'd suggest you take a look at the original paper....
https://www.ncbi.nlm.nih.gov/pubmed/24942700
Put simply,
Intensities are tidied up and , importantly, normalized globally across all samples.
From the paper about iBAQ (https://www.nature.com/articles/nature10098), MaxQuant computes protein intensities as the sum of all identified peptide intensities (maximum detector peak intensities of the peptide elution profile, including all peaks in the isotope cluster). Protein intensities were divided by the number of theoretically observable peptides (calculated by in silico protein digestion with a PERL script, all fully tryptic peptides between 6 and 30 amino acids were counted while missed cleavages were negelected).
Yes, Ilian Atanassov is right. iBAQ is the total intensities divided by the identified peptides for one protein.
It is hard to do absolute quantification of proteins. iBAQ works if all peptides were ionized and detected at the same efficency.
LFQ is very similar to the "protein intensities" used by iBAQ. It is normalized to exculde some "outliers" to best represent the ratio changes of different samples.
I think since the MaxQuant program can report intensity, LFQ and iBAQ, iBAQ can be used to compare the "molar" amount of different proteins, LFQ for comparison between samples, and intensity for some complex cases (e.g. some fractions were diluted or treated differently).
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