Fragmentation characteristics of glycopeptides

Mass spectrometric analysis of glycopeptides is an emerging strategy for analysis of glycosylation patterns. Here we present an approach using energy resolved collision induced decomposition (CID) spectra to determine structural features of glycopeptides. Fragmentation of multiply protonated glycopeptides proceeds by a series of competing charge separation processes by cleavage of a glycosidic bond, each producing two charged products: a singly charged, “B” type sugar (oxonium) ion, and a complementary high mass fragment. Energy requirements (activation energies) of these processes are similar to each other, and are far less, than that required for peptide fragmentation. At higher collision energies these first generation products fragment further, yielding a complex fragmentation pattern. Analysis of low energy spectra (those corresponding to ca. 50% survival yield) are straightforward; the ions observed correspond to structural features present in the oligosaccharide, and are not complicated by consecutive reactions. This makes it feasible to identify and distinguish antenna- and core-fucosylated isomers; antenna fucosylation usually suggests presence of the Lewis-X antigen. In general, analysis of the triply protonated molecules are most advantageous, where neutral losses and monosaccharide oxonium ion formation are less abundant

Distinguishing core and antenna fucosylated glycopeptides based on low energy tandem mass spectra

A straightforward approach has been developed to distinguish core and antenna fucosylation in glycopeptides. The method does not require derivatization, and can be easily adapted into a proteomics workflow. The key aspect is to use low collision energy CID (on a QTOF type instrument) when only single step fragmentation processes occur. Low collision energy should show the precursor ion as the largest peak in the spectrum; the survival yield should be ideally over 50%; and this is obtained at a collision energy ca. 30% of that typically used for proteomics. In such a case interfering processes like fucose migration or consecutive reactions are minimized. Core and antenna fucosylation can be discriminated using various ion abundance ratios. Low energy CID spectra are very “clean” (no chemical noise), and the ions used for locating the fucose are among the major peaks; making the method well suited for analytical work. Monitoring the change in the proportion of core and antenna fucosylation at the same glycosylation site is also feasible

Sensitive method for glycosaminoglycan analysis of tissue sections

A simple, isocratic HPLC method based on HILIC-WAX separation, has been developed for analyzing sulfated disaccharides of glycosaminoglycans (GAGs). To our best knowledge, this is the first successful attempt using this special phase in nano-HPLC-MS analysis. Mass spectrometry was based on negative ionization, improving both sensitivity and specificity. Detection limit for most sulfated disaccharides were approximately 1fmol; quantitation limits 10fmol. The method was applied for glycosaminoglycan profiling of tissue samples, using surface digestion protocols. This novel combination provides sufficient sensitivity for GAG disaccharide analysis, which was first performed using prostate cancer tissue microarrays. Preliminary results show that GAG analysis may be useful for identifying cancer related changes in small amounts of tissue samples (ca. 10mug)

A multipronged approach unravels unprecedented protein-protein interactions in the human 2-oxoglutarate dehydrogenase multienzyme complex

The human 2-oxoglutaric acid dehydrogenase complex (hOGDHc) plays a pivotal role in the tricarboxylic acid (TCA) cycle, and its diminished activity is associated with neurodegenerative diseases. The hOGDHc comprises three components, hE1o, hE2o, and hE3, and we recently reported functionally active E1o and E2o components, enabling studies on their assembly. No atomic-resolution structure for the hE2o component is currently available, so here we first studied the interactions in the binary subcomplexes (hE1o-hE2o, hE1o-hE3, and hE2o-hE3) to gain insight into the strength of their interactions and to identify the interaction loci in them. We carried out multiple physico-chemical studies, including fluorescence, hydrogen-deuterium exchange MS (HDX-MS), and chemical cross-linking MS (CL-MS). Our fluorescence studies suggested a strong interaction for the hE1o-hE2o subcomplex, but a much weaker interaction in the hE1o-hE3 subcomplex, and failed to identify any interaction in the hE2o-hE3 subcomplex. The HDX-MS studies gave evidence for interactions in the hE1o-hE2o and hE1o-hE3 subcomplexes comprising full-length components, identifying: (i) the N-terminal region of hE1o, in particular the two peptides 18YVEEM22 and 27ENPKSVHKSWDIF39 as constituting the binding region responsible for the assembly of the hE1o with both the hE2o and hE3 components into hOGDHc, an hE1 region absent in available X-ray structures; and (ii) a novel hE2o region comprising residues from both a linker region and from the catalytic domain as being a critical region interacting with hE1o. The CL-MS identified the loci in the hE1o and hE2o components interacting with each other

HPLC-MS METHOD FOR DESCRIBING HEPARAN-SULPHATE COMPOSITION OF TISSUE MICROARRAYS

Cancer research is a dynamically developing area of science and prostate cancer (PCa) is one of the most common types of cancer among men. Tissue biopsies are often used in mass spectrometry based biomarker research and have a great potential understanding biochemical mechanisms underlying diseases such as cancer. Tissue microarrays (TMA) consist of several biopsies (generally 1.5 mm in diameter) of different patients fixed on a microscope slide. The aim of our work was to develop and apply an advanced nanoLC-MS-based workflow to characterize glycosaminoglycans, in particular the degree of sulphation of heparane sulphate (HS) polysaccharide chains, occurring in tissues (PCa TMA cores). The first step of analysis is tissue surface digestion. HS chains were digested into disaccharides with bacterial lyase enzymes prior to the nanoLC-MS analysis. Thus the development and optimization of a chromatographic and MS method for the investigation of the HS disaccharides was performed with the mixture of the commercial standards of HS disaccharides. The separation method is based on the use of novel self-packed HILIC-WAX capillary columns; the effects of the ionic strength, the pH and the eluent strength were investigated and an isocratic separation method was found to be suitable for separating the HS disaccharides. The MS was operated in negative mode, and conditions were also optimized, eliminating fragmentation of the sulfate groups in the ion source. Relative ionization efficiency of the positional isomers was also determined. The limit of detection was ca. 1 fmol for each disaccharide and the limit of quantitation was between 10-50 fmol. The ratio of the different HS disaccharides was found to be a potentially useful indicator of PCa progression. A good correlation occurred between the cancer grade and sulphation patterns of heparan-sulphate chains; the ratio of doubly and triply sulfated disaccharides increased with cancer progression

In depth proteomic analysis of prostate cancer biopsies

Cancer research is among the most studied areas of science and prostate cancer (PCa) is one of the most common types of cancer among men. In this work we describe a detailed proteomics analysis of PCa tissue microarrays (TMAs) with our novel methodology. It is based on surface proteolytic digestion and proved to be capable of quantifying over 500 proteins from a single 1.5 mm diameter TMA core. We have compared the protein composition of tissues with various grades and stages of cancer. Samples from healthy and cancerous tissues were clearly distinguished and a good correlation with cancer grade was found. A well balanced study was carried out and over 100 proteins showed statistically significant abundance changes between various groups. During STRING evaluation up-regulation eg. in KEGG ribosome pathway and mRNA splicing could be observed

Investigation of genetic variants of alpha-1 acid glycoprotein by ultra-performance liquid chromatography-mass spectrometry

Genetic variants of human plasma alpha-1 acid glycoprotein (AGP) have been studied in cancer, compared with a group of healthy control. AGP has four genetic variants: AGP F1, F2, and S variants correspond to the ORM1 gene whereas AGP A corresponds to the ORM2 gene. The proportion of ORM1 and ORM2 variants were studied in plasma using a novel UPLC–MS method. Plasma total AGP level was 0.5 ± 0.2 g L−1 and the proportions of the ORM1 and ORM2 variants were 76.3 ± 8.2% and 23.7 ± 8.2%, respectively. In cancer plasma AGP levels increased fourfold and the proportion of ORM1 variants increased to 88.7 ± 6.8%. Changes in the proportion of genetic variants due to cancer were clearly significant, as shown by statistical analysis. Three different cancer types have been studied, lymphoma, melanoma, and ovarian cancer. The results did not show any difference depending on cancer type. The results indicate that, in accordance with prior expectations, the ORM1 variant is predominantly responsible for the acute-phase property of AGP