Peptides fragmentation

It is also important to remember that, in contrast to other methods, VolSurf can calculate descriptors for small, medium and large molecules, as well as for biopolymers such as DNA fragments, peptides and proteins. 

It would be complicating if not impossible having to obtain sequence information from such a spectrum without rules to follow. [138-141,146,147] The most abundant ions obtained from the fragmenting peptide ion usually belong to six series named a, b, and c if the proton (charge) is kept in the A-terminus or x, y, and z, respectively, where the proton is located in the C-terminal part. Within each se-... 

Extensive analysis of cyanogen bromide fragmented peptides of type I, III, and V collagens by MALDI-MS has shown that type V collagen from bovine skin is highly glycosylated, while type I and III collagens contain... 

Libraries can also be made from naturally occurring peptides (e.g. melanocortin [30] and somatostatin [31]) and their variants, or be derived from protein-fragments. The former have been employed mainly for the identification of peptide variants with unproved characteristics, and the latter for the identification of antigenic determinants present on targets, for example by selecting for binders to monoclonal antibodies specific for an antigen-fragment peptide library. 

The identified peptide fragments. Peptide fragments are shown as striped coil, with residues at the start and end of the peptides are numbered. Produced by Molscript [106], modified by R. Esneuf. 

Recent approaches to the amino acid analysis of foods require maceration of the sample, hydrolysis of the proteins with HC1, and filtration. The resulting material may still include proteins (and fragmented peptides), carbohydrates, salts, urea, and lipids. The solution is then passed through a small column of cation exchanger (with a nominal cross-linking of at least 8%) in... 

Given information on selective peptide cleavage and the sequences of fragment peptides, deduce the sequence of the original polypeptide. 

Davis TP, Porreca F, Burks TF, Dray A (1985) The proenkephalin A fragment, peptide E central processing and CNS activity in vivo. Eur J Pharmacol 777 177-183. 

The fragmentation of peptides can also be obtained by FTICR instruments. Besides the most commonly used activation method, namely CID, the activation can alternatively be performed without gas by infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD). These methods fragment peptide ions in the ICR cell by emitting a laser beam or electron beam, respectively. 

However, there remain important considerations in the MS analysis of peptides, as compared to those of proteins. These include the fact that the number of specific internal proteolytic (tryptic) sites are limiting and hence generally not available to produce specific peptide fragments. In this regard, MS analysis of proteins has relied heavily on the DNA sequence databases produced from both the genomic and the bioinformatic efforts to predict digested protein fragments. Peptides may be present in many different forms from their mature precursors, to partially processed precursors, to their fully... 

A method for cutting them specifically and reproducibly into fragments (peptides) which are small enough to be separated easily by chromatographic techniques (e.g., LC, capillary electrophoresis, 2D-TLC, electrophoresis, etc.)... 

Fig. 5 Schematic diagram of the siRNA delivery system. A cationic group is universal in all siRNA delivery systems to condense siRNA into nanosized complex. To release the siRNA from the endosome after endocytosis, an endosomal disrupting agent is also essential. PEG modification is also important to improve the pharmacokinetic profile of the complex, as well as to avoid the nonspecific uptake by RES. To achieve the targeted delivery to tumor cells, various ligands including antibody, antibody fragments, peptides, small molecules should be modified to the complex directly or via PEG as a linker...

Most of these algorithms are well adapted to fragment peptides by CDD, meanwhile the tool available at Starlab, Gent (http //genesisjug.ac.be/ nikos/) is adapted to fragment ions by PSD. Even though this tool was presented publicly in Siena 2000 [104], its scoring method has not yet been published. 

---