Direct analysis of α- and ß-chains of hemoglobins from mammalian blood samples by nanoESI mass spectrometry during in-capillary proteolytic digestion.

α- and ß-chains of hemoglobins derived from several species were analyzed directly from diluted blood samples by simultaneous in-capillary proteolytic digestion and nanoESI MS and MS/MS analysis. Starting from fresh or frozen and thawed blood samples, sequence coverages of >80% were usually obtained. Only 2 h after resuspension of a dried blood spot, human origin could be demonstrated from data obtained by in-capillary tryptic digestion, nanoESI mass spectrometric analysis, and data base search. A fast and facile differentiation of closely related species by hemoglobin-derived proteolytic "marker peptides" was demonstrated for Asian (Elephas maximus) and African elephants (Loxodonta africana). Finally, amino acid sequences deduced from collision-induced dissociation experiments during in-capillary proteolytic digestion of the corresponding blood samples allowed de novo sequencing of previously unknown sequences of hemoglobin chains of the Patagonian cavy (Dolichotum patagona) and the Persian gazelle (Gazella subgutturosa subgutturosa). 100% of the α-chain sequences and more than 85% of the ß-chain sequences were covered for both the species. Additionally, sequence data derived from tandem MS experiments obtained with the Q-Tof analyzer were confirmed by high resolution Fourier-transform ion cyclotron resonance mass spectrometric experiments. Accurate protein mass determination of the intact hemoglobin chains directly from the corresponding blood samples by use of a Fourier-transform ion cyclotron resonance mass spectrometer corroborated the deduced sequences of the respective α-chains. The present study demonstrates that in-capillary digestion allows fast characterization and/or sequencing of hemoglobin chains directly from blood samples.

IF/TA-related metabolic changes--proteome analysis of rat renal allografts.

BACKGROUND: Chronic allograft nephropathy, now more specifically termed interstitial fibrosis and tubular atrophy without evidence of any specific aetiology (IF/TA), is still an important cause of late graft loss. There is no effective therapy for IF/TA, in part due to the disease's multifactorial nature and its incompletely understood pathogenesis. METHODS: We used a differential in-gel electrophoresis and mass spectrometry technique to study IF/TA in a renal transplantation model. Dark Agouti (DA) kidneys were allogeneically transplanted to Wistar-Furth (DA-WF, aTX) rats. Syngeneic grafts (DA-DA, sTX) served as controls. Nine weeks after transplantation, blood pressure, renal function and electrolytes were studied, in addition to real-time PCR, western blot analysis, histology and immunohistochemistry. RESULTS: In contrast to sTX, the aTX developed IF/TA-dependent renal damage. Ten differentially regulated proteins were identified by 2D gel analysis and mass spectrometry, whereupon five proteins are mainly related to oxidative stress (aldo-keto reductase, peroxiredoxin-1, NAD(+)-dependent isocitrate dehydrogenase, iron-responsive element-binding protein-1 and serum albumin), two participate in cytoskeleton organization (l-plastin and ezrin) and three are assigned to metabolic functions (creatine kinase, ornithine aminotransferase and fructose-1,6-bisphosphatase). CONCLUSION: The proteins related to IF/TA and involved in oxidative stress, cytoskeleton organization and metabolic functions may correspond with novel therapeutic targets.

Structure analysis of N-glycoproteins.

General mass spectrometry-based strategies for analysis of N-glycosylated peptides are described. The well-established method utilizes Peptide-N-glycosidase F (PNGase F) for in-gel or in-solution release of N-linked glycans from the polypeptide chains (along with the conversion of the formerly N-glycosylated Asn to Asp), thus allowing separate analysis of glycan moieties and deglycosylated peptides. However, no assignment of individual glycans to a glycosylation site can be realized. Intact glycopeptides (i.e., proteolytic mixtures in which the glycan chains stay attached at their original glycosylation sites) can be analyzed either by a direct infusion or with HPLC separation prior to MALDI or ESI mass spectrometric analysis to provide both information on the glycan structure and glycosylation site in the same experiment. Several different strategies for efficient in-solution digestion of glycoproteins are described, such as proteolytic digestion in the electrospray capillary and simultaneous analysis of the resulting (glyco)peptides.

Structure elucidation of glycoproteins by direct nanoESI MS and MS/MS analysis of proteolytic glycopeptides.

Bovine ribonuclease B (RNAse B) and asialofetuin (FETUA) were subjected to in-capillary tryptic digest (Pohlentz et al. Proteomics. 2005, 5, 1758-1763) and the obtained glycopeptides were analyzed, respectively, by nanoelectrospray ionization mass spectrometry and collision-induced dissociation (CID) during the ongoing digest. For RNAse, B glycans of the high-mannose type (Man(4) to Man(9)) attached to either a tetra- or a hexapeptide containing the sole N-glycosylation site of the protein were detected. Glycopeptides derived from all three N-glycosylation sites of FETUA were observed, and the corresponding CID spectra proved the respective glycans to be oligosaccharides of the triantennary complex type. Moreover, an O-glycopeptide carrying Gal-GalNAc at T(280) could be unambiguously identified. An in-solution tryptic/chymotryptic digest of human transferrin (TRFE) was analyzed directly for glycopeptides subsequent to the addition of methanol and formic acid. Disialylated diantennary glycans were observed in glycopeptides of both N-glycosylation sites of TRFE. These results demonstrate the feasibility of direct structure determination of glycopeptides in proteolytic mixtures without any further refurbishment.