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In the case of whole proteins, multiple peptides from the parent protein can be used to gain confidence in the quantitation.
Multiple peptides from the alpha and beta chain of fibrin are capable to bind many HLA-DR alleles.
Thus, several clinical trials are ongoing in which multiple peptides from different proteins are targeted (http://www.clinicaltrial.gov).
Programmed -1 Ribosomal Frameshifting (-1 PRF) was first discovered in RNA viruses where it enables viral genomes to encode multiple peptides from a single mRNA [ 2].
To enhance the accuracy of the proteomics experiments, it would be beneficial to capture the same or multiple peptides from a protein by different binders.
Perform database search with the mass lists from MS/MS spectra of multiple peptides from the same protein using the Mascot software (http://www.matrixscience.com).com
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Multiple peptides derived from a single protein were included if PeptideProphet probability was greater than or equal to 0.85.
In addition to TRIM32, band A1 yielded multiple peptides obtained from ubiquitin (Fig. 7).
The multiple peptides assigned from the same spectra between algorithms might account for a part of the identification variations.
There were 24 peptides with significant (adjusted p-value < 0.01) differential peptide abundances between daytime and nighttime, including multiple peptides derived from secretogranin II, cocaine and amphetamine regulated transcript, and proprotein convertase subtilisin/kexin type 1 inhibitor.
This method is most robust for quantification at the protein level (as opposed to the peptide level) based on quantification of multiple peptides identified from the same protein, thus is less applicable for the study of endogenous neuropeptides (NPs), which are often present at very low levels and thus can be less reproducible in the frequency with which they trigger a MS/MS scan.
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