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Spektrometria mas w analizie białek i peptydów : znaczniki jonizacyjne

Bąchor R., Biernat M., Cebrat M., Kijewska M., Kluczyk A., Kuczer M., Paluch A., Waliczek M., Wierzbicka M., Stefanowicz P., Szewczuk Z.

Wiadomości Chemiczne

2018

[Z] 72, 7-8

609--633

High sensitivity, accuracy, and ability to provide structural information makes mass spectrometry (MS) the method of choice for both qualitative and quantitative analysis in proteome research. Peptide sequencing by tandem mass spectrometry (MS/MS) was successfully applied to discover new peptide sequences and modifications. Insufficient ionization of some peptides is one of the main limitations of MS- based peptide identification. The development of sensitive detection techniques for the efficient analysis of such samples is very important. Differences in ionizability cause difficulties in quantification studies, which could be overcome by derivatization of peptides to improve both the detectability and the selectivity of an analysis. Incorporation of ionization markers and isotopic labels (particularly the isobaric tags) is often used for this reason. Isobaric labeling reagents (including commercially available iTRAQ, TMT, DiLeu and DiART) have found a wide application in quantitative proteomics. Mass spectrometry is a very good tool for the determination of posttranslational modifications (PTMs), but the modified proteins are usually present in low concentrations. The development of ionization tags specific to a particular PTM and suitable for sensitive analysis of the modified proteins is required. For the analysis of phosphorylated peptides, a combination of β-elimination and the reaction of resulting α,β-dehydroamino acid residues with the nucleophilic thiol group could be used to detect a labile PTM. Such reaction may be used to introduce derivatizing reagents at the original site of phosphorylation, to enhance ionization in MS analysis. Glycation and glycosylation of proteins are other very important PTMs associated with many natural processes as well as diseases. We have designed and synthesized bifunctional quaternary ammonium salt derivatives of phenylboronic acids for selective detection of carbohydrates and peptide-derived Amadori products by ESI-MS. The attachment of a fixed charge (e.g. in a form of a quaternary ammonium salt) to the amino groups in peptides leads to the enhancement of a precursor ion signal in mass spectra. We have developed several new QAS-containing ionization reagents including bicyclic tags with DABCO, ABCO or azoniaspiro groups. It is worth noting that 2,4,6-substituted pyrylium salts react with amino groups in peptides introducing a stable positive charge and improve peptide detection by MS. The newly developed ionization tags were successfully applied for the analysis of OBOC combinatorial libraries as well as for studying possible biomarkers of preeclampsia, a pregnancy disorder.

Multi-stage Informatic Technology

Węgrzyn S., Znamirowski L.

Archiwum Informatyki Teoretycznej i Stosowanej

2005

T. 17, z. 3

173-188

In the paper, the production processes of a nano-products fabrication based on multi-stage informatic technology applying the concept of so called "gluey matrix" are described. In the first stage, an "intermediate product" is created, with linear, molecular structure identical to linear sequence in a final product. In the next stages, that flat, linear structure will convert into a spatial shape of molecules representing the final product. The operations performed in those systems are based on nanotechnologies or a "bottom-up" creation of the product. This approach to the product creation requires knowledge about the product molecular constitution and the phenomena obsewed on the surface of molecules and atoms, which allow for a design of a proper, "gluey matrix". This matrix introduced into a mixture of freely moving molecules (building blocks) concentrates and integrates the building blocks on the surface of matrix forming the needed intermediate product. In the next stages, the intermediate product created and next detached from the surface of gluey matrix is a substrate for the creation of appropriate final product by affecting the intermediate product with various external stimuli, assuring the proper conformational modifications.

W pracy scharakteryzowano procesy produkcyjne stosowane w wytwarzaniu nanostruktur bazujące na wielostopniowej informatycznej technologii wytwarzania przy zastosowaniu koncepcji tzw. "macierzy lepkiej". W trakcie pierwszej fazy procesu jest wytwarzany półprodukt, którego liniowa, molekularna struktura jest taka sama jak w produkcie finalnym. W kolejnych fazach, ta liniowa struktura jest modyfikowana przestrzennie w celu otrzymania pożądanej konformacji produktu finalnego. W pracy przedstawiono różne warianty tego typu procesów. Macierz lepka wykorzystywana jest do syntezy struktury molekularnej na bazie podstawowych struktur elementarnych. Modyfikacje konformacji półproduktów realizowane są oddziaływaniem środowiska w którym realizuje się proces produkcyjny, na półprodukt otrzymany w pierwszej fazie procesu.