Peptide redundancy

Merte J. and Nichols R. (2002) Drosophila melanogaster FMRFamide-containing peptides redundant or diverse functions Peptides 23, 209-220. 

As is the case with identifications based on protein molecular masses, it appears that the use of tryptic or other peptide masses as the basis for identification is extended with difficulty to mixtures of microorganisms. This reflects unpredictable suppression. Another limitation is redundancy of peptide masses across several microorganisms. For example, the most abundant proteins (SASPs), and thus the most abundant peptides, in spores of Bacillus anthracis and the closely related pesticide Bacillus thuringiensis have extensive sequence homology.25,82... 

Even though the MALDI peptide mass mapping technique is very powerful, it has limitations. It requires well-separated proteins, is less sensitive than identifications based on electrospray tandem mass spectrometry, can only identify proteins whose complete sequences are available in databases, and does not produce redundant information. 

Several vasoactive peptides provide examples where one angiogenic pathway gives way to another, thereby maintaining angiogenesis. This plasticity of angiogenic pathways emphasizes the need to extend studies in normal tissues by undertaking research on pathological samples, since factors that are important in one may be redundant in the other. 

Note Some of this information is redundant peptides Tryp 1 and CNBr 1 would be sufficient for unambiguous sequence determination. In addition, in such a simple case, with only two peptides from each cleavage reaction, we could determine the sequence from either one of these cleavages alone using the fact that the carboxyl sides of Met and Lys are the sites of cleavage with CNBr and trypsin, respectively. 

Normally the spectra show several incomplete series of ions that produce redundant data and make the spectrum very complex and difficult to interpret. The peptide sequence can be deduced even if several incomplete series of ions are present, provided that there are other series of ions present and as long as there are overlaps in the deduced sequence information. 

Without any doubt, mass spectrometry is now the most efficient way to identify proteins [75-78], The method is based on comparison of the data obtained from the mass spectrometry with those predicted for all the proteins contained in a database. The efficiency of the method results from the development of mass spectrometry into a rapid and sensitive method to analyse peptides and proteins and also from the availability of larger and larger databases. In October 2006, these databases contained more than 2400000 non-redundant sequences. Furthermore, the data obtained from genomic sequences after translation in the six lecture frames also can be used. The databases based on expressed sequence tags (ESTs) are another usable source for search. They are composed of sequences based on cDNA fast sequencing. They are limited to short lengths, about 300 bases, and contain many errors but they correspond to coding sequences. Despite their defects, they are very useful for identification of proteins by mass spectrometry [79]. 

Both target peptides and signal peptides direct the precursor to the proper membrane by interaction with membrane-associated factors. In yeast, target peptides interact directly with functionally redundant receptors in the mitochondrial outer membrane (reviewed in Baker and Schatz,... 

Chen, H., Rejtar, T., Andreev, V., Moskovets, E. and Kaiger, B.L. (2005a) Enhanced characterization of complex proteomic samples using LC-MALDI MS/MS exclusion of redundant peptides from MS/MS analysis in replicate mns. Anal. Chem. 77, 7816-7825. 

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