Peak identification and quantification by proteomic mass spectrogram decomposition

Recent advances in liquid chromatography/mass spectrometry (LC/MS) technology have notably improved the sensitivity, resolution, and speed of proteome analysis, resulting in increasing demand for more sophisticated algorithms to interpret complex mass spectrograms. Here, we propose a novel statistical method that we call proteomic mass spectrogram decomposition (ProtMSD) for joint identification and quantification of peptides and proteins. Given the proteomic mass spectrogram and the reference mass spectra of all possible peptide ions associated with proteins as a dictionary, our method directly estimates the temporal intensity curves of those peptide ions, i.e., the chromatograms, under a group sparsity constraint without using the conventional careful pre-processing (e.g., thresholding and peak picking). We show that the accuracy of protein identification was significantly improved by using the protein-peptide hierarchical relationships, the isotopic distribution profiles and predicted retention times of peptide ions and the pre-learned mass spectra of noise. In the analysis of E. coli cell lysate, our ProtMSD showed excellent agreement (3277 peptide ions (94.79%) and 493 proteins (98.21%)) with the conventional cascading approach to identification and quantification based on Mascot and Skyline. This is the first attempt to use a matrix decomposition technique as a tool for LC/MS-based joint proteome identification and quantification.

P078 Efficiency of evaluating the expression of Toll-like receptors 2, 4, 6 and proteins proteomic profiling as integral indicators for predicting the risk of early relapse of ulcerative colitis

Background Success was made in the study of TLR in congenital and adaptive immunity, which determined a new look at immune processes at ulcerative colitis (UC). Modern achievements of proteomic methods of analysis research allow to define molecular characteristics of the inflammation in colon mucosa of patients with UC. Methods The study included 86 patients with UC, an average age of 39.0 ± 1.4 years. Groups: 1–15 (17.4%) patients with distal form of UC, 2–42 (48%) left-sided form, 3–29 (33.7%) patients with total UC. The expression of TLR on peripheral blood monocytes was determined in the immunofluorescence test. Two-colour analysis was performed on a flow-through laser cytofluorimeter (Cytomics FC500, Beckman Coulte). The percentage of monocytes (CD14 + cells) carrying TLR2, TLR4, TLR6 on their surface was assessed. The separation of proteins of colon mucosa was based on technologies of IEF, SDS–PAGE, 2DPAGE (Bruker, USA). The getting of mass spectrogram was determined by matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF-MS/MS, Ultraflex II, Bruker, USA). Statistical analysis was performed using the software Statistica 10.0 (Statsoft). Results The direct average relationship was established between the number of monocytes expressing CD14 + CD282 +, CD14 + CD284 +, CD14 + CD286 + and the area of inflammation (r = 0.49, r = 0.55, r = 0.42, p < 0.05). The nonlinear regression equation was used. Calculation example: the risk of recurrence UC = exp (−26.1 + (0.4) × TLR 2)/(1 + exp (−26.1 + (0.4) × TLR 2)), χ2 = 130, 59, p < 0.0001. Thus, when the number of monocytes expressing TLR2 is not more than 60%, the risk of recurrence of the UC is not more than 11%, with values above 70%, the probability of recurrence exceeds 80%. We identified potentially new molecular markers of the early relapse of ulcerative colitis: SMAD2 activates the transcription of TFG1β and leads to development of fibrosis in colon submucosa in patients with UC; significant decrease of the expression of PPARγ promotes the activation of STAT and AP-1 signalling pathways that promotes the increase of the synthesis of IL-2,6,8,12,TNFα, the activity of immune and inflammation processes in colon mucosa; the reduction of expression of β-defensin-1 in cells of colon mucosa are accompanied with increased expression of CCR6, that promotes the formation of inflammatory infiltrates in colonic submucosa in UC. Conclusion Expression of TLR 2,4,6 in blood monocytes (the risk of recurrence UC ratio) and new protein molecular markers of colon mucosa (SMAD2, PPARγ and apoС-III) can be used as a tool for prediction of early relapse UC.

P390 New features of molecular diagnostics of the regulation of molecular apoptotic pathway in ulcerative colitis

Background The incidence rate of ulcerative colitis (UC) in Russia is 5–30 cases per 100,000 per year. Molecular pathways of the UC development are not clear. The purpose of the work was to study the molecular interactions of the apoptotic pathway in patients with UC. Methods The clinical trial included 92 patients with UC. The clinical presentation of UC depends on the extent of involvement: distal colitis, extensive colitis; the severity of the disease. Criteria of the diagnosis of UC corresponded to ECCO Consensus. Mucosal specimens were graded according to grades 0, 1, 2, 3. The separation of proteins of colon mucosa was based on technologies of IEF, SDS-PAGE, 2DPAGE, by standard sets (MB-HIC C8 Kit, MB-IMAC Cu, MB-Wax Kit, Bruker, USA). The getting of mass-spectrogram was determined by matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF-MS/MS, Ultraflex II, Bruker, USA). Statistical analysis was performed using the software Statistica 10.0 (Statsoft). Results HSP2 controls the apoptosis of colonocytes and immune response in damaged colon mucosa by Bcl-2 and IL-17, and is also responsible for the resistance to therapeutic strategies. Anti-apoptotic functions of HSP27 is possible through the interaction with DAXX7, the activation of Akt and the inhibition of the apoptosis. HSP47 interacts with collagen I, II, III, IV and V types, that contributes to the launch of autoimmune process in UC. Caspase 8 protects colonocytes from TNFα-induced cell death through necroptosis mechanism via the blockade of the expression of RIP3. Significant decrease of the expression of PPARγ promotes the activation of STAT and AP-1 signalling pathways, that promotes the increase of the synthesis of IL-2, -6, -8, -12, TNFα, matrix metalloproteinases, the activity of immune and inflammation processes in the colon mucosa. Results of qualitative proteomic analysis in patients with UC (Tab.) Conclusion Proteomic analysis has demonstrated the cascade with caspases 8, 9, 10, the release of cytochrome C from mitochondria, which interacts with Apaf-1, causing activation of caspase-9 in UC colon mucosa. TNF-α activates of initiator caspase-2, -8, and -10 in the apoptotic pathway. The NF-kB pathway induces cellular inhibitors of apoptosis, which function as specific caspase inhibitors in UC colonic mucosa.

P016 Efficiency of evaluating the expression of Toll-like receptors 2, 4, 6 and proteins proteomic profiling as integral indicators for predicting the risk of early relapse of ulcerative colitis

Background Success was made in the study of TLR in congenital and adaptive immunity, which determined a new look at immune processes at ulcerative colitis (UC). Modern achievements of proteomic methods of analysis research allow to define molecular characteristics of the inflammation in colon mucosa of patients with UC. Methods The study included 86 patients with UC, an average age of 39.0 ± 1.4 years. Groups: 1–15 (17.4%) patients with distal form of UC, 2–42 (48%) left-sided form, 3–29 (33.7%) patients with total UC. The expression of TLR on peripheral blood monocytes was determined in the immunofluorescence test. Two-colour analysis was performed on a flowthrough laser cytofluorimeter (Cytomics FC500, Beckman Coulte). The percentage of monocytes (CD14 + cells) carrying TLR2, TLR4, and TLR6 on their surface was assessed. The separation of proteins of colon mucosa was based on technologies of IEF, SDS–PAGE, 2DPAGE, by standard sets (MB-HIC C8 Kit, MB-IMAC Cu, MB-Wax Kit, Bruker, USA). The getting of mass spectrogram was determined by matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF-MS/MS, Ultraflex II, Bruker, USA). Statistical analysis was performed using the software Statistica 10.0 (Statsoft). Results The direct average relationship was established between the number of monocytes expressing CD14 + CD282 +, CD14 + CD284 +, CD14 + CD286 + and the area of inflammation (r = 0.49, r = 0.55, r = 0.42, p < 0.05). The nonlinear regression equation was used. Calculation example: the risk of recurrence UC = exp (−26.1 + (0.4) × TLR 2)/(1 + exp (−26.1 + (0.4) × TLR 2)), χ2 = 130, 59, p < 0.0001. Thus, when the number of monocytes expressing TLR2 is not more than 60%, the risk of recurrence of the UC is not more than 11%, with values above 70%, the probability of recurrence exceeds 80%. We identified potentially new molecular markers of the early relapse of ulcerative colitis: SMAD2 activates the transcription of TFG1β and leads to development of fibrosis in colon submucosa in patients with UC; significant decrease of the expression of PPARγ promotes the activation of STAT and AP-1 signalling pathways that promotes the increase of the synthesis of IL-2, 6, 8, 12, TNFα, the activity of immune and inflammation processes in colon mucosa; the reduction of expression of β-defensin-1 in cells of colon mucosa is accompanied with increased expression of CCR6 that promotes the formation of inflammatory infiltrates in colonic submucosa in UC. Conclusion Expression of TLR 2, 4, 6 in blood monocytes (the risk of recurrence UC ratio) and new protein molecular markers of colon mucosa (SMAD2, PPARγ, and apoС-III) can be used as a tool for prediction of early relapse UC.

Dual inhibitors of urease and carbonic anhydrase-II from Iris species

Twenty seven (1–27) known natural organic compounds were isolated for first time from two species of Iris, i.e. loczyi and Iris unguicularis. The structures of these compounds were deduced from the spectral data of NMR, IR, and mass spectrogram. These were evaluated against urease and carbonic anhydrase inhibition studies. For carbonic anhydrase-II inhibition studies, these compounds were evaluated by biochemical mechanism based in vitro bio-assay. Some compounds showed significant inhibition against CA-II enzyme. Compartively, compound (12) showed IC50 value of 17.60 ± 0.08 μM against urease enzyme, while compound (3) was found to be most active against carbonic anhydrase-II, having an IC50 value of 66.27 ± 0.89 μM. Izalpinin (3), 5,7-dihydroxy-2′,6-dimethoxyisoflavone (9), 4′,5,7-trihydroxy-6-methoxyflavanone (16), 4′,5,7-trihydroxy-3′,8-dimethoxyflavanone (20), 8-methoxyeriodictyol (21), and mangiferin (26) were found to be dual inhibitors of both the enyzmes. The most active compounds were docked using Autodock Vina and i-GEMDOCK softwares. The docking and in-vitro results are in agreement which showed secondary interactions with the enzymes. The compounds can serve as therapeutic agents to treat urease and carbonic anhydrase associated disorders.

Application of PCA-RBF Method to QSRR Studies on Hydrocarbon in FCC Gasoline with PCA-RBF

A novel Artificial Neutral Network (ANN) algorithm based on Principle component analysis(PCA) is proposed and applied to predicted the retention index of a series of hydrocarbons in FCC gasoline. The PCA technology is utilized to preprocess the mass spectrogram of FCC gasoline for parameter selection and to reduce the input of prediction model, which thus improve the input factors and eliminates the correlation among the inputs. Then new sample data are input into radial basis function-artificial neutral network(RBF-ANN) to construct the prediction model.156 compounds were divided into two subsets. RSM of training set and testing set is 0.9958 and 0.9991, respectively. The satisfactory results were obtained.