Nano-reversed Phase Liquid Chromatography Research Articles

An Integrated Comprehensive Peptidomics and In Silico Analysis of Bioactive Peptide-Rich Milk Fermented by Three Autochthonous Cocci Strains.

Bioactive peptides (BPs) are molecules of paramount importance with great potential for the development of functional foods, nutraceuticals or therapeutics for the prevention or treatment of various diseases. A functional BP-rich dairy product was produced by lyophilisation of bovine milk fermented by the autochthonous strains Lactococcus lactis subsp. lactis ZGBP5-51, Enterococcus faecium ZGBP5-52 and Enterococcus faecalis ZGBP5-53 isolated from the same artisanal fresh cheese. The efficiency of the proteolytic system of the implemented strains in the production of BPs was confirmed by a combined high-throughput mass spectrometry (MS)-based peptidome profiling and an in silico approach. First, peptides released by microbial fermentation were identified via a non-targeted peptide analysis (NTA) comprising reversed-phase nano-liquid chromatography (RP nano-LC) coupled with matrix-assisted laser desorption/ionisation-time-of-flight/time-of-flight (MALDI-TOF/TOF) MS, and then quantified by targeted peptide analysis (TA) involving RP ultrahigh-performance LC (RP-UHPLC) coupled with triple-quadrupole MS (QQQ-MS). A combined database and literature search revealed that 10 of the 25 peptides identified in this work have bioactive properties described in the literature. Finally, by combining the output of MS-based peptidome profiling with in silico bioactivity prediction tools, three peptides (75QFLPYPYYAKPA86, 40VAPFPEVFGK49, 117ARHPHPHLSF126), whose bioactive properties have not been previously reported in the literature, were identified as potential BP candidates.

Top-down mass spectrometry for characterizing the low molecular weight proteome of canine osteosarcoma cell phenotypes.

Osteosarcoma (OS) is the most common primary malignant tumor of bone, which occupying about 20% of all bone cancers. To increase understanding of the biology of OS, we developed and evaluated a top-down mass spectrometry approach to detect, identify and quantify low molecular weight (MW) proteins (i.e., 1 kDa < MW < 30 kDa) in osteosarcoma cells. Top-down proteomic (TDP) data was acquired using reversed phase nano-liquid chromatography in conjunction with high-resolution mass spectrometry and resulted in the assignment of 328 proteins and 820 proteoforms or degradation products with high confidence. Eight post-translational modifications (PTMs) were identified in the present study, including N-terminal acetylation, lysine acetylation, succinylation, malonylation, serine/tyrosine phosphorylation, histidine methylation and N-acetylleucine. We confirmed that a truncated N-terminal proteoform lost 73 Da of mass through removal of the N-terminal Met (-131 Da), acetylation of the second amino acid (+42 Da), and Met oxidation (+16 Da). The results showed that the levels of proteoforms/biodegradable peptides correlated with the metastatic phenotypes of osteosarcoma cell lines. This study demonstrates the benefits of TDP for the characterization and relative quantification of proteoforms with relevance to OS biology and the potential of small molecular weight proteoforms to serve as a still underappreciated source of biomarkers.

Pilot Study of the Ex Vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma

Background: Leukocytes are key cellular effectors of inflammation in asthma and understanding their function in this disease is of crucial importance. Blood leukocytes reflect the actions of their counterparts in the lungs and they can be obtained through minimal invasive procedures as part of the peripheral blood. Objective: The aim of the study was to identify proteins in blood leukocyte proteomes that respond to ex vivo treatment by prednisone in order to pinpoint candidates for predictive biomarkers in corticosteroid- responsive asthma. Methods: The study included five children diagnosed with asthma and five healthy children. After the ex vivo treatment of blood samples with prednisone, lysis of erythrocytes was performed and proteins were extracted from the remaining leukocytes by ultrasonic disintegration. Protein extracts were analyzed by reversed phase nano-liquidchromatography–tandem mass spectrometry (LC–MS/MS). Results: The stimulation of asthmatics' leukocytes with prednisone has led to an increase in the levels of FYB (fold change 3.4) and LYZ (fold change 2.2) with a statistical significance of p&lt;0.005. The two proteins with expressions significantly altered upon the prednisone treatment should be further explored as tools to evaluate the patient's response before therapy administration, especially when lung function measurements are not possible, as is the case with young pediatric patients. Conclusion: The approach that entails ex vivo response of blood leukocytes to therapeutics can facilitate asthma management and help overcome the need for therapeutic adjustments in a clinical setting.

Separation methods in single-cell proteomics: RPLC or CE?

Cellular heterogeneity is commonly investigated using single-cell genomics and transcriptomics to investigate biological questions such as disease mechanism, therapeutic screening, and genomic and transcriptomic diversity between cellular populations and subpopulations at the single-cell level. Single-cell mass spectrometry (MS)-based proteomics enables the high-throughput examination of protein expression at the single-cell level with wide applicability, and with spatial and temporal resolution, applicable to the study of cellular development, disease, effect of treatment, etc. The study of single-cell proteomics has lagged behind genomics and transcriptomics largely because proteins from single-cell samples cannot be amplified as DNA and RNA can using well established techniques such as PCR. Therefore, analytical methods must be robust, reproducible, and sensitive enough to detect the very small amount of protein within a single cell. To this end, nearly every step of the proteomics process has been extensively altered and improved to facilitate the proteomics analysis of single cells including cell counting and sorting, lysis, protein digestion, sample cleanup, separation, MS data acquisition, and data analysis. Here, we have reviewed recent advances in single-cell protein separation using nano reversed phase liquid chromatography (nRPLC) and capillary electrophoresis (CE) to inform application driven selection of separation techniques in the laboratory setting.

Proteomic Landscape of Adeno-Associated Virus (AAV)-Producing HEK293 Cells.

Adeno-associated viral (AAV) vectors are widely used for gene therapy, providing treatment for diseases caused by absent or defective genes. Despite the success of gene therapy, AAV manufacturing is still challenging, with production yields being limited. With increased patient demand, improvements in host cell productivity through various engineering strategies will be necessary. Here, we study the host cell proteome of AAV5-producing HEK293 cells using reversed phase nano-liquid chromatography and tandem mass spectrometry (RPLC-MS/MS). Relative label-free quantitation (LFQ) was performed, allowing a comparison of transfected vs. untransfected cells. Gene ontology enrichment and pathway analysis revealed differential expression of proteins involved in fundamental cellular processes such as metabolism, proliferation, and cell death. Furthermore, changes in expression of proteins involved in endocytosis and lysosomal degradation were observed. Our data provides highly valuable insights into cellular mechanisms involved during recombinant AAV production by HEK293 cells, thus potentially enabling further improvements of gene therapy product manufacturing.

Characterization of Kinase Activity By Phosphoproteomics in Myeloid Cell Lines for Identification of Driving Oncogenic Pathways

Introduction: Myelodysplastic syndromes (MDS) are heterogeneous disorders caused by sequential accumulation of genetic lesions in haematopoietic stem cells (HSC). MDS are characterized by dysplasia, ineffective haematopoiesis and a propensity to evolve towards acute myeloid leukemia (AML). Based on the recent advances in next generation sequencing, our understanding of the genetic background of myeloid neoplasms has dramatically increased. However, clonal heterogeneity, genetic interactions, and clonal evolution remain enigmatic phenomena of oncogenesis and important investigational challenges to be addressed in the post-genomic era.Aim and objectives: The aim of this project was to build a bioinformatic pipeline to integrate phosphoproteomic data with genetic information in order to characterize targettable kinase-activities of involved oncogenic pathways. Our objective was to establish a network analysis of the kinase-substrate relationship in myeloid cell lines first, before moving into primary cells. Here, we present data on the ongoing phosphoproteome characterization and the inferred kinase-activity from five myeloid cell lines.Methods: The five myeloid cell lines K562 (erythroid), NB4 (promyelocytic), THP1 (monocytic), OCI-AML3 (myelomonocytic) and MOLM13 (monocytic) were used. These cell lines contain distinct oncogenes, such as BCR-ABL1, PML-RARalpha, MLL-MLLT3, mutated NPM1 and FLT3-ITD, respectively. Cytogenetic analysis and next generation sequencing, using a myeloid driver gene panel of Ion Torrent, were performed for genetic characterization (Table 1). Phosphoproteomes were enriched using Titanium-dioxide (TiO2) and samples were analyzed in triplicates by reversed-phase nano liquid chromatography coupled to tandem-mass spectrometry (nanoLC-MS2). Raw data was analyzed using MaxQuant software and further processed with R . For kinase-activity enrichment analysis (KAEA), we integrated all substrate-kinase datasets from five databases 1) PhosphoSitePlus, 2) Human Protein Reference Database, 3) Regulatory Network in Protein Phosphorylation, 4) The Signaling Network Open Resource and 5) phosphor.ELM . The SetRank R-package was employed for KAEA with p-value and FDR cutoffs set at 0.05.Results: We identified 15'698, 14'087, 13'969, 13'993 and 14'201 unique phosphopeptides corresponding to 3'536, 3'363, 3'411, 3'410 and 3'403 unique phosphoproteins, respectively.KAEA identified 77 different kinases across the five cell lines (Table 2). In the heat-map of the KAEA, phenotypically related cell lines clustered together and unique kinase-activity patterns emerged for each cell line (Figure 1). Two cell lines are driven by oncogenic kinases; K562 by BCR-ABL1 and MOLM13 by FLT3-ITD. An ABL1-kinase signal was detectable from 2 different databases in K562 as well as additional downstream kinases of ABL1, including mTOR and MAPK. We could not enrich for the FLT3-kinase in MOLM-13, due to lack of representation in the currently available substrate-kinase databases. However, our pipeline was able to identify the activity of downstream kinases of FLT3, including AKT1/PKB and MAPK1.Conclusion: Our bioinformatic pipeline was able to detect unique phosphoproteins and enrich for kinase-activities in five distinct myeloid cell lines. Moreover, it reproduced an expected pattern of kinase-activities for two relevant driving oncogenic kinases. These promising results remain still limited by insufficient quantification and incompleteness of available databases. We expect to further improve on quantification and annotation by using heavy labeled cell lines (SILAC) as well as kinase-motif analysis, respectively. This may allow us to perform unsupervised characterization of involved oncogenic pathways and to proceed into the analysis of primary cells. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Identification and semi-relative quantification of intact glycoforms of human chorionic gonadotropin alpha and beta subunits by nano liquid chromatography-Orbitrap mass spectrometry

The human chorionic gonadotropin (hCG) protein belongs to a family of glycoprotein hormones called gonadotropins. It is a heterodimer made of two non-covalently linked subunits. The α-subunit structure, hCGα, has 2 N-glycosylation sites, while the beta subunit, hCGβ, has 2 N- and 4 O-glycosylation sites. This leads to numerous glycoforms. A method based on the analysis of hCG glycoforms at the intact level by nano-reversed phase liquid chromatography coupled to high resolution mass spectrometry (nanoLC-HRMS) with an Orbitrap analyzer was previously developed using a recombinant hCG-based drug, Ovitrelle®, as standard. It allowed the detection of about 30 hCGα glycoforms, but didn't allow the detection of hCGβ glycoforms. This method was thus here significantly modified (addition of a pre-concentration step of the sample to increase the sample volume from 70 nl to 1 µl, optimization of the gradient slope and the nature and content of the acidic additive in the mobile phase). It led to an improvement of the separation of hCGα and hCGβ glycoforms, which allowed for the first time the detection of 33 hCGβ glycoforms at intact level. In addition, a higher number of hCGα glycoforms (42 in total, i.e. a 40% increase) was detected. The figures of merit of this new method were next assessed. The relative standard deviations (RSDs) of the retention time ranged between 0.02 and 0.95% (n = 3), with an average value of 0.36% for the alpha glycoforms and between 0.01 and 1.08% (n = 3) with an average value of 0.23% for the beta glycoforms. The RSDs of the relative peak area measured on the extracted ion chromatogram of each glycoform were below 20% (n = 3), with an average value of 9.8%, thus allowing semi-relative quantification. Therefore, this method has a high potential for rapid quality control aiming for the detection and comparison of glycoforms present in glycoprotein-based pharmaceutical preparations.

Comprehensive Profiling of the Native and Modified Peptidomes of Raw Bovine Milk and Processed Milk Products.

Bovine milk contains a variety of endogenous peptides, partially formed by milk proteases that may exert diverse bioactive functions. Milk storage allows further protease activities altering the milk peptidome, while processing, e.g., heat treatment can trigger diverse chemical reactions, such as Maillard reactions and oxidations, leading to different posttranslational modifications (PTMs). The influence of processing on the native and modified peptidome was studied by analyzing peptides extracted from raw milk (RM), ultra-high temperature (UHT) milk, and powdered infant formula (IF) by nano reversed-phase liquid chromatography coupled online to electrospray ionization (ESI) tandem mass spectrometry. Only unmodified peptides proposed by two independent software tools were considered as identified. Thus, 801 identified peptides mainly originated from αS- and β-caseins, but also from milk fat globular membrane proteins, such as glycosylation-dependent cell adhesion molecule 1. RM and UHT milk showed comparable unmodified peptide profiles, whereas IF differed mainly due to a higher number of β-casein peptides. When 26 non-enzymatic posttranslational modifications (PTMs) were targeted in the milk peptidomes, 175 modified peptides were identified, i.e., mostly lactosylated and a few hexosylated or oxidized peptides. Most modified peptides originated from αS-caseins. The numbers of lactosylated peptides increased with harsher processing.

Microfluidic water-assisted trap focusing method for ultra-large volume injection in reversed-phase nano-liquid chromatography coupled to electron ionization tandem-mass spectrometry

Herein we present an efficient, column-switching method that relies on a custom-made T-union passive diffusion micromixer to assist water dilution and promote trap solute focusing of a high sample volume dissolved in pure organic solvent using a 0.075mm i.d. nano-LC column. This method allows injecting 20 μL (or higher) of sample volume, speeding up the analysis time, with a 400-fold increase of the limits of quantitation for selected compounds. Five pesticides in different media were used as model compounds, and the analyses were carried out with a triple quadrupole mass spectrometer equipped with a Liquid Electron Ionization (LEI) LC-MS interface working in multiple reaction monitoring (MRM) mode. The system microfluidics were investigated using COMSOL modeling software. Robustness of the entire system was evaluated using a post-extraction addition soil extracts with limits of detection values spanning from 0.10 to 0.45µg/L. Reproducible results in terms of peak area, peak shape, and retention times were achieved in soil matrix. Repeatability test on peak area variations were lower than 10%.

Homocysteinylated alpha 1 antitrypsin as an antigenic target of autoantibodies in seronegative rheumatoid arthritis patients

Rheumatoid arthritis (RA) is a chronic autoimmune disease and rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPA) are the most frequently detected autoantibodies (autoAbs). To date, more than 20% of RA cases are still defined as seronegative forms (seronegative RA, SN-RA). The aim of this study was to identify new antigenic targets of autoAbs in RA patients, which can also be recognized in SN-RA. Using a proteomic approach, we tested sera from SN-RA patients by analyzing synovial fluid (SF) proteins from these patients. Sera from SN-RA patients revealed a strong reactive spot, corresponding to alpha 1 antitrypsin (A1AT). Reverse-phase nanoliquid chromatography and tandem mass spectrometry (Matrix Assisted Laser Desorption/Ionization-Time Of Flight, MALDI-TOF/TOF) confirmed the presence of A1AT in SF and showed that homocysteinylation was one of the post-translational modifications of A1AT. Homocysteinylated (Hcy)-A1AT immunoprecipitated from SN-RA patients' SFs and in vitro modified Hcy-A1AT were used as antigens by Enzyme-Linked ImmunoSorbent Assay (ELISA) to test the presence of specific autoAbs in sera from 111 SN-RA patients, 132 seropositive (SP)-RA patients, and from 95 patients with psoriatic arthritis, 40 patients with osteoarthritis, and 41 healthy subjects as control populations. We observed that a large portion of SN-RA patients (75.7%), and also most of SP-RA patients' sera (87.1%) displayed anti-Hcy-A1AT autoAbs (anti-HATA). Native A1AT was targeted at a lower rate by SP-RA patients autoAbs, while virtually no SN-RA patients' sera showed the presence of anti-native A1AT autoAbs. In conclusion, anti-HATA can be considered potential biomarkers for RA, also in the SN forms. The discovery of novel autoAbs targeting specific autoantigens can represent higher clinic significance for all RA patients’ population.

Characterization of carbaryl-degrading strain Bacillus licheniformis B-1 and its hydrolase identification.

Pesticides introduced inadvertently or deliberately into environment by anthropogenic activity have caused growing global public concern, therefore the search of approaches for elimination of such xenobiotics should be encouraged. A cypermethrin-degrading bacterial strain Bacillus licheniformis B-1 was found to efficiently degrade carbaryl in LB medium at concentrations of 50-300mg L-1 within 48h, during which temperature and pH played important roles as reflected by increase in pollutant depletion. A stimulatory effect of Fe3+ and Mn2+ on microbial growth was observed, whereas Cu2+ caused inhibition of degradation. Results showed that 1-naphthol was a major transformation product of carbaryl which was further metabolised. An approximately 29kDa carbaryl-degrading enzyme was purified from B-1 with 15.93-fold purification and an overall yield of 6.02% was achieved using ammonium sulphate precipitation, DEAE-Sepharose CL-6B anion-exchange chromatography and Sephadex G-100 gel filtration. The enzyme was identified through nano reversed-phase liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry as a phosphodiesterase (PDE). This is the first report on the characterization of carbaryl-degrading by Bacillus spp. and the role of a PDE in carbaryl-detoxifying. Also, strain B-1 showed versatile in carbosulfan, isoprocarb and chlorpyrifos degradation, demonstrating as ideal candidate for environment bioremediation.

Evaluation of reversed-phase nano liquid chromatography conditions by using reversed-phase thin layer chromatography based on Hansen solubility parameters for the analysis of amphiphilic glycosylsphingolipid transformations

Pulse chase analysis is often used in investigating dynamics of cellular substances. Fluorescently labeled lactosyl sphingosine molecule is useful in chasing its transformation, however the analysis of such metabolites in attomole level is of extreme difficult due to the presence of large amount of endogenous amphiphilic molecules such as glycosphingolipids, sphingomyerin, and glycerophospholipids. Nano LC suites for analyzing the attomole scale metabolites, therefore removal of endogenous substances prior to nano LC and finding appropriate nano LC conditions are necessary. Thus, we focused on the solubility of fluorescent BODIPY-labeled lactosylsphingosine (Lac-Sph-BODIPY) to identify suitable solvents to remove endogenous compounds. In this study, we evaluated solvents by using C18 thin layer chromatography (RP TLC). The mobility (Rf) of Lac-Sph-BODIPY against several solvent mixtures on RP TLC were plotted against polarity and hydrogen bonding capability followed by Hansen solubility parameters (HSPs). The optimum solvent mixture with Rf = 0.3 ± 0.1 was chosen for elimination of endogenous phospholipids on a ZrO2-SiO2 cartridge column and subsequent separation by nano LC. Efficient removal of endogenous phospholipids was demonstrated, and good resolution in nano LC analysis of Lac-Sph-BODIPY extracted from Chinese hamster ovary (CHO)-K1 cells was achieved. It was also shown that the amount of exogenously added compound was important in the investigation of metabolites using cultured cells.

Automated SPE and nanoLC–MS analysis of somatostatin

ABSTRACTPlasma peptides are widely used in clinical diagnosis and therapy monitoring. Our aim was an efficient system development for the enrichment of small, low abundant peptides from plasma by robotized sample preparation. The automation of SPE yields additional time saving and improves system robustness and repeatability. Automation is based on combining a Waters SPE kit with Oasis HLB sorbent and a multichannel liquid handling workstation with cheap commercially available electronic devices such as a programmable logic controller (PLC) and an AVR controller. Reversed phase nano liquid chromatography coupled with a sensitive quadrupole time of flight mass spectrometer (QTOF MS) was used for the quantitative determination of somatostatin (SST). We quantified SST from mouse plasma, where lower limit of detection (LLOD) and lower limit of quantification (LLOQ) were 2.5 and 8.3 fmol/ml, respectively. We investigated linearity of response, accuracy, precision, recovery, reproducibility and stability of SST during both short-term sample processing and long-term storage. This method allows reliable quantification of plasma peptides. The developed automated sample preparation solid phase extraction method can be easily and conveniently adopted for different volumes and amounts of sample in routine analysis using controlled vacuum. The highest advantage is enhanced reproducibility, which makes it suitable for the investigations of large sample cohorts in clinical studies.

Proteomics of Colorectal Cancer in a Genomic Context: First Large-scale Mass Spectrometry-Based Analysis from the Cancer Genome Atlas.

Cancer is a disease caused by DNA alterations that make cells grow in an uncontrolled way. Identifying the alterations in each tumor's complete set of DNA (the genome) and its functionally relevant protein complement (the proteome) is expected to increase our understanding of how such changes interact to drive the disease. This global molecular information will help lay a foundation for improving cancer prevention, early detection, and treatment. In the past decade, mass spectrometry (MS)3 technology and (bio)informatics tools have matured to the extent that they can provide high-throughput, comprehensive protein inventories of cells, tissues, and biofluids, even when present at low concentrations (1), paving the way for large-scale profiling of clinical samples. The integration of proteomic and genomic data in which MS/MS data are searched against customized databases of individually matched DNA/RNA sequence data, referred to as proteogenomics, provides a more comprehensive view of the molecular determinants that drive cancer than genomic analysis alone and may help identify the most important targets for cancer detection and intervention. Six years ago, the first report on the genomic characterization of glioblastoma was published by the Cancer Genome Atlas (TCGA) network. A research team of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has now assembled an MS-based inventory of protein expression and variants in 95 colon and rectal tumors (2) that were previously characterized by the TCGA project. The authors focused on the question of how gene alterations identified in previous analyses of the same samples are expressed at the protein level. To enable a comprehensive and in-depth analysis of colorectal tumors, the CPTAC team used a label-free, next-generation proteomics approach based on basic and reversed-phase nano-liquid chromatography coupled to high-resolution tandem MS (2). The tandem MS data were analyzed by an innovative bioinformatics pipeline that was developed in-house for stringent …

Molecular signatures that correlate with induction of lens regeneration in newts: lessons from proteomic analysis.

BackgroundAmphibians have the remarkable ability to regenerate missing body parts. After complete removal of the eye lens, the dorsal but not the ventral iris will transdifferentiate to regenerate an exact replica of the lost lens. We used reverse-phase nano-liquid chromatography followed by mass spectrometry to detect protein concentrations in dorsal and ventral iris 0, 4, and 8 days post-lentectomy. We performed gene expression comparisons between regeneration and intact timepoints as well as between dorsal and ventral iris.ResultsOur analysis revealed gene expression patterns associated with the ability of the dorsal iris for transdifferentiation and lens regeneration. Proteins regulating gene expression and various metabolic processes were enriched in regeneration timepoints. Proteins involved in extracellular matrix, gene expression, and DNA-associated functions like DNA repair formed a regeneration-related protein network and were all up-regulated in the dorsal iris. In addition, we investigated protein concentrations in cultured dorsal (transdifferentiation-competent) and ventral (transdifferentiation-incompetent) iris pigmented epithelial (IPE) cells. Our comparative analysis revealed that the ability of dorsal IPE cells to keep memory of their tissue of origin and transdifferentiation is associated with the expression of proteins that specify the dorso-ventral axis of the eye as well as with proteins found highly expressed in regeneration timepoints, especially 8 days post-lentectomy.ConclusionsThe study deepens our understanding in the mechanism of regeneration by providing protein networks and pathways that participate in the process.Electronic supplementary materialThe online version of this article (doi:10.1186/s40246-014-0022-y) contains supplementary material, which is available to authorized users.

Chromatographic assessment of two hybrid monoliths prepared via epoxy-amine ring-opening polymerization and methacrylate-based free radical polymerization using methacrylate epoxy cyclosiloxane as functional monomer

Two kinds of hybrid monolithic columns were prepared by using methacrylate epoxy cyclosiloxane (epoxy-MA) as functional monomer, containing three epoxy moieties and one methacrylate group. One column was in situ fabricated by ring-opening polymerization of epoxy-MA and 1,10-diaminodecane (DAD) using a porogenic system consisting of isopropanol (IPA), H2O and ethanol at 65°C for 12h. The other was prepared by free radical polymerization of epoxy-MA and ethylene dimethacrylate (EDMA) using 1-propanol and 1,4-butanediol as the porogenic solvents at 60°C for 12h. Two hybrid monoliths were investigated on the morphology and chromatographic assessment. Although two kinds of monolithic columns were prepared with epoxy-MA, their morphologies looked rather different. It could be found that the epoxy-MA–DAD monolith possessed higher column efficiencies (25,000–34,000plates/m) for the separation of alkylbenzenes than the epoxy-MA–EDMA monolith (12,000–13,000plates/m) in reversed-phase nano-liquid chromatography (nano-LC). Depending on the remaining epoxy or methacrylate groups on the surface of two pristine monoliths, the epoxy-MA–EDMA monolith could be easily modified with 1-octadecylamine (ODA) via ring-opening reaction, while the epoxy-MA–DAD monolith could be modified with stearyl methacrylate (SMA) via free radical reaction. The chromatographic performance for the separation of alkylbenzenes on SMA-modified epoxy-MA–DAD monolith was remarkably improved (42,000-54,000 plates/m) when compared with that on pristine epoxy-MA–DAD monolith, while it was not obviously enhanced on ODA-modified epoxy-MA–EDMA monolith when compared with that on pristine epoxy-MA–EDMA monolith. The enhancement of the column efficiency of epoxy-MA–DAD monolith after modification might be ascribed to the decreased mass-transfer resistence. The two kinds of hybrid monoliths were also applied for separations of six phenols and seven basic compounds in nano-LC.

Proteins with potential role in analgesic effect of spinal cord stimulation on neuropathic pain

Abstract Aims We aimed to find proteins of relevance to the prolonged analgesic effect of spinal cord stimulation (SCS) for patients with neuropathic pain. Methods The proteomes of cerebrospinal fluid (CSF) from 14 neuropathic pain patients using spinal cord stimulation (SCS) was compared to the CSF proteomes of the same patients when not using the stimulator. Samples were analyzed by dimethyl label and label free shotgun proteomics approach. Samples were prepared by immunoaffinity fractionation and then separated by reversed phase nanoliquid chromatography coupled to an electrospray ionization source and analyzed by high resolution tandem mass spectrometry. The proteins were comparatively quantified on the peptide level and ranked based on numbers of regulated peptides. Then the dimethyl and label free analysis results were combined. In order to group proteins by function and interactions, a functional enrichment network analysis was performed using the String (Search Tool for the Retrieval of Interacting Genes/Proteins) database on all significantly differentially expressed proteins. Results We found 87 differentially expressed proteins. Network analysis showed a high level of enrichment in interactions between the proteins involved in platelet degranulation and wound healing with p-values 2.48E−11 and 4.58E−08. We also recognized two additional clusters related to complement and coagulation cascades and neuropeptides. None of these proteins have been implicated in SCS mechanism previously. Conclusions Up- and down-regulations of immunological proteins and neuropeptides may explain the prolonged relief of neuropathic pain obtained after SCS. These findings contribute a new basis for understanding of SCS analgesic mechanism in human neuropathic pain. Further verification studies of these initial findings are needed.

SAT0574 Peptidomic Analysis of Cartilage Secretome for the Discovery of Early OA Biomarkers

BackgroundThe low-molecular-weight subset of the cartilage proteome (also termed cartilage peptidome) may have a diagnostic potential in osteoarthritis (OA) research, not yet fully exploited.ObjectivesThe aim of this study is to...

Determination of site selectivity of different carcinogens for preferential mutational hot spots in oligonucleotide fragments by ion-pair reversed-phase nano liquid chromatography tandem mass spectrometry.

Ion-pair reversed-phase nano liquid chromatography coupled with nanospray ion trap mass spectrometry was used to investigate site selectivity of the known carcinogens N-acetoxy-2-acetylaminofluorene, N-hydroxy-4-aminobiphenyl and (+/-)-anti-benzo[a]pyrene diol epoxide with the synthetic double-strand 14-mer long oligonucleotide fragment of the p53 gene containing two mutational hot-spot codons (5'-P-ACC155 CGC156 GTC157 CGC158 GC/5'-GCG CGG ACG CGG GT). The investigation was performed using a monolithic polystyrene divinylbenzene capillary column and triethylammonium bicarbonate as an ion-pair reagent. The exact location of the carcinogen on the modified oligonucleotide backbone was determined using characteristic collision-induced dissociation fragmentation patterns obtained under negative-ion mode ionization. In all these cases, the adducted, isomeric oligonucleotides formed were chromatographically resolved and structural identification was performed without any prior deoxyribonucleic acid cleavage or hydrolysis. The knowledge of the site specificity of a carcinogen, especially at purported mutational hot spots, is of paramount importance (1) in establishing the identity of biomarkers for an early risk assessment of the formed DNA adducts, (2) developing repair mechanisms for the formed carcinogen adducted DNA, and (3) understanding the nature of the covalent bond formed and mapping the frequency of the adduction process.

Molecular signatures that correlate with induction of lens regeneration in newts: lessons from proteomic analysis

Amphibians have the remarkable ability to regenerate missing body parts. After complete removal of the eye lens, the dorsal but not the ventral iris will transdifferentiate to regenerate an exact replica of the lost lens. We used reverse-phase nano-liquid chromatography followed by mass spectrometry to detect protein concentrations in dorsal and ventral iris 0, 4, and 8 days post-lentectomy. We performed gene expression comparisons between regeneration and intact timepoints as well as between dorsal and ventral iris. Our analysis revealed gene expression patterns associated with the ability of the dorsal iris for transdifferentiation and lens regeneration. Proteins regulating gene expression and various metabolic processes were enriched in regeneration timepoints. Proteins involved in extracellular matrix, gene expression, and DNA-associated functions like DNA repair formed a regeneration-related protein network and were all up-regulated in the dorsal iris. In addition, we investigated protein concentrations in cultured dorsal (transdifferentiation-competent) and ventral (transdifferentiation-incompetent) iris pigmented epithelial (IPE) cells. Our comparative analysis revealed that the ability of dorsal IPE cells to keep memory of their tissue of origin and transdifferentiation is associated with the expression of proteins that specify the dorso-ventral axis of the eye as well as with proteins found highly expressed in regeneration timepoints, especially 8 days post-lentectomy. The study deepens our understanding in the mechanism of regeneration by providing protein networks and pathways that participate in the process.