Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 20

Mass Spectrometry Related Abstracts

20 Automatic Threshold Search for Heat Map Based Feature Selection: A Cancer Dataset Analysis

Authors: Carlos Huertas, Reyes Juarez-Ramirez

Abstract:

Public health is one of the most critical issues today; therefore, there is great interest to improve technologies in the area of diseases detection. With machine learning and feature selection, it has been possible to aid the diagnosis of several diseases such as cancer. In this work, we present an extension to the Heat Map Based Feature Selection algorithm, this modification allows automatic threshold parameter selection that helps to improve the generalization performance of high dimensional data such as mass spectrometry. We have performed a comparison analysis using multiple cancer datasets and compare against the well known Recursive Feature Elimination algorithm and our original proposal, the results show improved classification performance that is very competitive against current techniques.

Keywords: Cancer, Biomarker Discovery, Mass Spectrometry, Feature selection

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19 Coupling of Microfluidic Droplet Systems with ESI-MS Detection for Reaction Optimization

Authors: Detlev Belder, Julia R. Beulig, Stefan Ohla

Abstract:

In contrast to off-line analytical methods, lab-on-a-chip technology delivers direct information about the observed reaction. Therefore, microfluidic devices make an important scientific contribution, e.g. in the field of synthetic chemistry. Herein, the rapid generation of analytical data can be applied for the optimization of chemical reactions. These microfluidic devices enable a fast change of reaction conditions as well as a resource saving method of operation. In the presented work, we focus on the investigation of multiphase regimes, more specifically on a biphasic microfluidic droplet systems. Here, every single droplet is a reaction container with customized conditions. The biggest challenge is the rapid qualitative and quantitative readout of information as most detection techniques for droplet systems are non-specific, time-consuming or too slow. An exception is the electrospray mass spectrometry (ESI-MS). The combination of a reaction screening platform with a rapid and specific detection method is an important step in droplet-based microfluidics. In this work, we present a novel approach for synthesis optimization on the nanoliter scale with direct ESI-MS detection. The development of a droplet-based microfluidic device, which enables the modification of different parameters while simultaneously monitoring the effect on the reaction within a single run, is shown. By common soft- and photolithographic techniques a polydimethylsiloxane (PDMS) microfluidic chip with different functionalities is developed. As an interface for the MS detection, we use a steel capillary for ESI and improve the spray stability with a Teflon siphon tubing, which is inserted underneath the steel capillary. By optimizing the flow rates, it is possible to screen parameters of various reactions, this is exemplarity shown by a Domino Knoevenagel Hetero-Diels-Alder reaction. Different starting materials, catalyst concentrations and solvent compositions are investigated. Due to the high repetition rate of the droplet production, each set of reaction condition is examined hundreds of times. As a result, of the investigation, we receive possible reagents, the ideal water-methanol ratio of the solvent and the most effective catalyst concentration. The developed system can help to determine important information about the optimal parameters of a reaction within a short time. With this novel tool, we make an important step on the field of combining droplet-based microfluidics with organic reaction screening.

Keywords: Microfluidics, Mass Spectrometry, Screening, droplet, organic reaction

Procedia PDF Downloads 157
18 Comparison of Physicochemical Properties of Catfish Myofibrillar and Sarcoplasmic Protein Hydrolysates and Characterization of Their Bioactive Peptides

Authors: Leila Najafian

Abstract:

Sarcoplasmic protein hydrolysates (SPHs) and myofibrillar protein hydrolysates (MPHs) from patin (Pangasius sutchi) were produced using two types of proteases: Papain and Alcalase. 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) radical scavenging activities and metal chelating activity assays for antioxidant activities were carried out on the SPHs and MPHs. The hydrolysates were isolated and purified by ultrafiltration, gel filtration and reverse phase high-performance liquid chromatography (RP-HPLC) and liquid chromatography with tandem mass spectrometry detection (LC-MS/MS) was used in identifying peptide sequences. The results showed that when the DH of MPHs increased, the protein solubility increased, while the highest amount of the protein solubility of SPHs was after 60 min incubation. The effect of DH on antioxidant activities of SPHs and MPHs was investigated. Among the hydrolysates, papain-MPH and Alcalase-SPH, which had the highest antioxidant activities, were purified. The potent fractions obtained from RP-HPLC of sarcoplasmic (SI 3 fraction) and myofibrillar (MI 4 fraction) hydrolysates showed the highest DPPH radical scavenging activity. The FVNQPYLLYSVHMK peptide for MPH and the LVVDIPAALQHA peptide for SPH exhibited the highest antioxidant activity. The presence of hydrophobic and hydrophilic amino acids, namely leucine (L), valine (V), phenylalanine (F), histidine (H) and proline (P), in the peptide sequences of SPH and MPH are believed to contribute to high antioxidant activity. Hence, SPH and MPH from patin have the potential as a natural functional ingredient in food and pharmaceutical industry.

Keywords: Mass Spectrometry, Protein Hydrolysates, patin (Pangasius sutchi), antioxidative peptides

Procedia PDF Downloads 146
17 Qualitative Characterization of Proteins in Common and Quality Protein Maize Corn by Mass Spectrometry

Authors: Benito Minjarez, Jesse Haramati, Yury Rodriguez-Yanez, Florencio Recendiz-Hurtado, Juan-Pedro Luna-Arias, Salvador Mena-Munguia

Abstract:

During the last decades, the world has experienced a rapid industrialization and an expanding economy favoring a demographic boom. As a consequence, countries around the world have focused on developing new strategies related to the production of different farm products in order to meet future demands. Consequently, different strategies have been developed seeking to improve the major food products for both humans and livestock. Corn, after wheat and rice, is the third most important crop globally and is the primary food source for both humans and livestock in many regions around the globe. In addition, maize (Zea mays) is an important source of protein accounting for up to 60% of the daily human protein supply. Generally, many of the cereal grains have proteins with relatively low nutritional value, when they are compared with proteins from meat. In the case of corn, much of the protein is found in the endosperm (75 to 85%) and is deficient in two essential amino acids, lysine, and tryptophan. This deficiency results in an imbalance of amino acids and low protein content; normal maize varieties have less than half of the recommended amino acids for human nutrition. In addition, studies have shown that this deficiency has been associated with symptoms of growth impairment, anemia, hypoproteinemia, and fatty liver. Due to the fact that most of the presently available maize varieties do not contain the quality and quantity of proteins necessary for a balanced diet, different countries have focused on the research of quality protein maize (QPM). Researchers have characterized QPM noting that these varieties may contain between 70 to 100% more residues of the amino acids essential for animal and human nutrition, lysine, and tryptophan, than common corn. Several countries in Africa, Latin America, as well as China, have incorporated QPM in their agricultural development plan. Large parts of these countries have chosen a specific QPM variety based on their local needs and climate. Reviews have described the breeding methods of maize and have revealed the lack of studies on genetic and proteomic diversity of proteins in QPM varieties, and their genetic relationships with normal maize varieties. Therefore, molecular marker identification using tools such as mass spectrometry may accelerate the selection of plants that carry the desired proteins with high lysine and tryptophan concentration. To date, QPM maize lines have played a very important role in alleviating the malnutrition, and better characterization of these lines would provide a valuable nutritional enhancement for use in the resource-poor regions of the world. Thus, the objectives of this study were to identify proteins in QPM maize in comparison with a common maize line as a control.

Keywords: Mass Spectrometry, corn, QPM, tryptophan

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16 Aflatoxins Characterization in Remedial Plant-Delphinium denudatum by High-Performance Liquid Chromatography–Tandem Mass Spectrometry

Authors: Nadeem A. Siddique, Mohd Mujeeb, Kahkashan

Abstract:

Introduction: The objective of the projected work is to study the occurrence of the aflatoxins B1, B2, G1and G2 in remedial plants, exclusively in Delphinium denudatum. The aflatoxins were analysed by high-performance liquid chromatography–tandem quadrupole mass spectrometry with electrospray ionization (HPLC–MS/MS) and immunoaffinity column chromatography were used for extraction and purification of aflatoxins. PDA media was selected for fungal count. Results: A good quality linear relationship was originated for AFB1, AFB2, AFG1 and AFG2 at 1–10 ppb (r > 0.9995). The analyte precision at three different spiking levels was 88.7–109.1 %, by means of low per cent relative standard deviations in each case. Within 5 to7 min aflatoxins can be separated using an Agilent XDB C18-column. We found that AFB1 and AFB2 were not found in D. denudatum. This was reliable through exceptionally low figures of fungal colonies observed after 6 hr of incubation. The developed analytical method is straightforward, be successfully used to determine the aflatoxins. Conclusion: The developed analytical method is straightforward, simple, accurate, economical and can be successfully used to find out the aflatoxins in remedial plants and consequently to have power over the quality of products. The presence of aflatoxin in the plant extracts was interrelated to the least fungal load in the remedial plants examined.

Keywords: Mass Spectrometry, liquid chromatography, aflatoxins, delphinium denudatum

Procedia PDF Downloads 67
15 De-Novo Structural Elucidation from Mass/NMR Spectra

Authors: Ismael Zamora, Elisabeth Ortega, Tatiana Radchenko, Guillem Plasencia

Abstract:

The structure elucidation based on Mass Spectra (MS) data of unknown substances is an unresolved problem that affects many different fields of application. The recent overview of software available for structure elucidation of small molecules has shown the demand for efficient computational tool that will be able to perform structure elucidation of unknown small molecules and peptides. We developed an algorithm for De-Novo fragment analysis based on MS data that proposes a set of scored and ranked structures that are compatible with the MS and MSMS spectra. Several different algorithms were developed depending on the initial set of fragments and the structure building processes. Also, in all cases, several scores for the final molecule ranking were computed. They were validated with small and middle databases (DB) with the eleven test set compounds. Similar results were obtained from any of the databases that contained the fragments of the expected compound. We presented an algorithm. Or De-Novo fragment analysis based on only mass spectrometry (MS) data only that proposed a set of scored/ranked structures that was validated on different types of databases and showed good results as proof of concept. Moreover, the solutions proposed by Mass Spectrometry were submitted to the prediction of NMR spectra in order to elucidate which of the proposed structures was compatible with the NMR spectra collected.

Keywords: Mass Spectrometry, Structure Elucidation, NMR, De Novo

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14 Full Characterization of Heterogeneous Antibody Samples under Denaturing and Native Conditions on a Hybrid Quadrupole-Orbitrap Mass Spectrometer

Authors: Rowan Moore, Kai Scheffler, Eugen Damoc, Jennifer Sutton, Aaron Bailey, Stephane Houel, Simon Cubbon, Jonathan Josephs

Abstract:

Purpose: MS analysis of monoclonal antibodies (mAbs) at the protein and peptide levels is critical during development and production of biopharmaceuticals. The compositions of current generation therapeutic proteins are often complex due to various modifications which may affect efficacy. Intact proteins analyzed by MS are detected in higher charge states that also provide more complexity in mass spectra. Protein analysis in native or native-like conditions with zero or minimal organic solvent and neutral or weakly acidic pH decreases charge state value resulting in mAb detection at higher m/z ranges with more spatial resolution. Methods: Three commercially available mAbs were used for all experiments. Intact proteins were desalted online using size exclusion chromatography (SEC) or reversed phase chromatography coupled on-line with a mass spectrometer. For streamlined use of the LC- MS platform we used a single SEC column and alternately selected specific mobile phases to perform separations in either denaturing or native-like conditions: buffer A (20 % ACN, 0.1 % FA) with Buffer B (100 mM ammonium acetate). For peptide analysis mAbs were proteolytically digested with and without prior reduction and alkylation. The mass spectrometer used for all experiments was a commercially available Thermo Scientific™ hybrid Quadrupole-Orbitrap™ mass spectrometer, equipped with the new BioPharma option which includes a new High Mass Range (HMR) mode that allows for improved high mass transmission and mass detection up to 8000 m/z. Results: We have analyzed the profiles of three mAbs under reducing and native conditions by direct infusion with offline desalting and with on-line desalting via size exclusion and reversed phase type columns. The presence of high salt under denaturing conditions was found to influence the observed charge state envelope and impact mass accuracy after spectral deconvolution. The significantly lower charge states observed under native conditions improves the spatial resolution of protein signals and has significant benefits for the analysis of antibody mixtures, e.g. lysine variants, degradants or sequence variants. This type of analysis requires the detection of masses beyond the standard mass range ranging up to 6000 m/z requiring the extended capabilities available in the new HMR mode. We have compared each antibody sample that was analyzed individually with mixtures in various relative concentrations. For this type of analysis, we observed that apparent native structures persist and ESI is benefited by the addition of low amounts of acetonitrile and formic acid in combination with the ammonium acetate-buffered mobile phase. For analyses on the peptide level we analyzed reduced/alkylated, and non-reduced proteolytic digests of the individual antibodies separated via reversed phase chromatography aiming to retrieve as much information as possible regarding sequence coverage, disulfide bridges, post-translational modifications such as various glycans, sequence variants, and their relative quantification. All data acquired were submitted to a single software package for analysis aiming to obtain a complete picture of the molecules analyzed. Here we demonstrate the capabilities of the mass spectrometer to fully characterize homogeneous and heterogeneous therapeutic proteins on one single platform. Conclusion: Full characterization of heterogeneous intact protein mixtures by improved mass separation on a quadrupole-Orbitrap™ mass spectrometer with extended capabilities has been demonstrated.

Keywords: Mass Spectrometry, Monoclonal Antibodies, Peptide Mapping, UHPLC, disulfide bond analysis, intact analysis, native analysis, post-translational modifications, sequence variants, size exclusion chromatography, therapeutic protein analysis

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13 Characterization of Dota-Girentuximab Conjugates for Radioimmunotherapy

Authors: Tais Basaco, Stefanie Pektor, Josue A. Moreno, Matthias Miederer, Andreas Türler

Abstract:

Radiopharmaceuticals based in monoclonal anti-body (mAb) via chemical linkers have become a potential tool in nuclear medicine because of their specificity and the large variability and availability of therapeutic radiometals. It is important to identify the conjugation sites and number of attached chelator to mAb to obtain radioimmunoconjugates with required immunoreactivity and radiostability. Girentuximab antibody (G250) is a potential candidate for radioimmunotherapy of clear cell carcinomas (RCCs) because it is reactive with CAIX antigen, a transmembrane glycoprotein overexpressed on the cell surface of most ( > 90%) (RCCs). G250 was conjugated with the bifunctional chelating agent DOTA (1,4,7,10-Tetraazacyclododecane-N,N’,N’’,N’’’-tetraacetic acid) via a benzyl-thiocyano group as a linker (p-SCN-Bn-DOTA). DOTA-G250 conjugates were analyzed by size exclusion chromatography (SE-HPLC) and by electrophoresis (SDS-PAGE). The potential site-specific conjugation was identified by liquid chromatography–mass spectrometry (LC/MS-MS) and the number of linkers per molecule of mAb was calculated using the molecular weight (MW) measured by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The average number obtained in the conjugates in non-reduced conditions was between 8-10 molecules of DOTA per molecule of mAb. The average number obtained in the conjugates in reduced conditions was between 1-2 and 3-4 molecules of DOTA per molecule of mAb in the light chain (LC) and heavy chain (HC) respectively. Potential DOTA modification sites of the chelator were identified in lysine residues. The biological activity of the conjugates was evaluated by flow cytometry (FACS) using CAIX negative (SKRC-18) and CAIX positive (SKRC-52). The DOTA-G250 conjugates were labelled with 177Lu with a radiochemical yield > 95% reaching specific activities of 12 MBq/µg. The stability in vitro of different types of radioconstructs was analyzed in human serum albumin (HSA). The radiostability of 177Lu-DOTA-G250 at high specific activity was increased by addition of sodium ascorbate after the labelling. The immunoreactivity was evaluated in vitro and in vivo. Binding to CAIX positive cells (SK-RC-52) at different specific activities was higher for conjugates with less DOTA content. Protein dose was optimized in mice with subcutaneously growing SK-RC-52 tumors using different amounts of 177Lu- DOTA-G250.

Keywords: Radiopharmaceuticals, Mass Spectrometry, Monoclonal Antibody, radioimmunotheray, renal cancer

Procedia PDF Downloads 159
12 Production of Insulin Analogue SCI-57 by Transient Expression in Nicotiana benthamiana

Authors: Adriana Muñoz-Talavera, Ana Rosa Rincón-Sánchez, Abraham Escobedo-Moratilla, María Cristina Islas-Carbajal, Miguel Ángel Gómez-Lim

Abstract:

The highest rates of diabetes incidence and prevalence worldwide will increase the number of diabetic patients requiring insulin or insulin analogues. Then, current production systems would not be sufficient to meet the future market demands. Therefore, developing efficient expression systems for insulin and insulin analogues are needed. In addition, insulin analogues with better pharmacokinetics and pharmacodynamics properties and without mitogenic potential will be required. SCI-57 (single chain insulin-57) is an insulin analogue having 10 times greater affinity to the insulin receptor, higher resistance to thermal degradation than insulin, native mitogenicity and biological effect. Plants as expression platforms have been used to produce recombinant proteins because of their advantages such as cost-effectiveness, posttranslational modifications, absence of human pathogens and high quality. Immunoglobulin production with a yield of 50% has been achieved by transient expression in Nicotiana benthamiana (Nb). The aim of this study is to produce SCI-57 by transient expression in Nb. Methodology: DNA sequence encoding SCI-57 was cloned in pICH31070. This construction was introduced into Agrobacterium tumefaciens by electroporation. The resulting strain was used to infiltrate leaves of Nb. In order to isolate SCI-57, leaves from transformed plants were incubated 3 hours with the extraction buffer therefore filtrated to remove solid material. The resultant protein solution was subjected to anion exchange chromatography on an FPLC system and ultrafiltration to purify SCI-57. Detection of SCI-57 was made by electrophoresis pattern (SDS-PAGE). Protein band was digested with trypsin and the peptides were analyzed by Liquid chromatography tandem-mass spectrometry (LC-MS/MS). A purified protein sample (20µM) was analyzed by ESI-Q-TOF-MS to obtain the ionization pattern and the exact molecular weight determination. Chromatography pattern and impurities detection were performed using RP-HPLC using recombinant insulin as standard. The identity of the SCI-57 was confirmed by anti-insulin ELISA. The total soluble protein concentration was quantified by Bradford assay. Results: The expression cassette was verified by restriction mapping (5393 bp fragment). The SDS-PAGE of crude leaf extract (CLE) of transformed plants, revealed a protein of about 6.4 kDa, non-present in CLE of untransformed plants. The LC-MS/MS results displayed one peptide with a high score that matches SCI-57 amino acid sequence in the sample, confirming the identity of SCI-57. From the purified SCI-57 sample (PSCI-57) the most intense charge state was 1069 m/z (+6) on the displayed ionization pattern corresponding to the molecular weight of SCI-57 (6412.6554 Da). The RP-HPLC of the PSCI-57 shows the presence of a peak with similar retention time (rt) and UV spectroscopic profile to the insulin standard (SCI-57 rt=12.96 and insulin rt=12.70 min). The collected SCI-57 peak had ELISA signal. The total protein amount in CLE from transformed plants was higher compared to untransformed plants. Conclusions: Our results suggest the feasibility to produce insulin analogue SCI-57 by transient expression in Nicotiana benthamiana. Further work is being undertaken to evaluate the biological activity by glucose uptake by insulin-sensitive and insulin-resistant murine and human cultured adipocytes.

Keywords: Mass Spectrometry, insulin analogue, Nicotiana benthamiana, transient expression

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11 Statistical Pattern Recognition for Biotechnological Process Characterization Based on High Resolution Mass Spectrometry

Authors: S. Fröhlich, M. Herold, M. Allmer

Abstract:

Early stage quantitative analysis of host cell protein (HCP) variations is challenging yet necessary for comprehensive bioprocess development. High resolution mass spectrometry (HRMS) provides a high-end technology for accurate identification alongside with quantitative information. Hereby we describe a flexible HRMS assay platform to quantify HCPs relevant in microbial expression systems such as E. Coli in both up and downstream development by means of MVDA tools. Cell pellets were lysed and proteins extracted, purified samples not further treated before applying the SMART tryptic digest kit. Peptides separation was optimized using an RP-UHPLC separation platform. HRMS-MSMS analysis was conducted on an Orbitrap Velos Elite applying CID. Quantification was performed label-free taking into account ionization properties and physicochemical peptide similarities. Results were analyzed using SIEVE 2.0 (Thermo Fisher Scientific) and SIMCA (Umetrics AG). The developed HRMS platform was applied to an E. Coli expression set with varying productivity and the corresponding downstream process. Selected HCPs were successfully quantified within the fmol range. Analysing HCP networks based on pattern analysis facilitated low level quantification and enhanced validity. This approach is of high relevance for high-throughput screening experiments during upstream development, e.g. for titer determination, dynamic HCP network analysis or product characterization. Considering the downstream purification process, physicochemical clustering of identified HCPs is of relevance to adjust buffer conditions accordingly. However, the technology provides an innovative approach for label-free MS based quantification relying on statistical pattern analysis and comparison. Absolute quantification based on physicochemical properties and peptide similarity score provides a technological approach without the need of sophisticated sample preparation strategies and is therefore proven to be straightforward, sensitive and highly reproducible in terms of product characterization.

Keywords: Pattern Recognition, Mass Spectrometry, Process Analytical Technology, process characterization, MVDA

Procedia PDF Downloads 118
10 Comparative Proteomic Profiling of Planktonic and Biofilms from Staphylococcus aureus Using Tandem Mass Tag-Based Mass Spectrometry

Authors: Arifur Rahman, Ardeshir Amirkhani, Honghua Hu, Mark Molloy, Karen Vickery

Abstract:

Introduction and Objectives: Staphylococcus aureus and coagulase-negative staphylococci comprises approximately 65% of infections associated with medical devices and are well known for their biofilm formatting ability. Biofilm-related infections are extremely difficult to eradicate owing to their high tolerance to antibiotics and host immune defences. Currently, there is no efficient method for early biofilm detection. A better understanding to enable detection of biofilm specific proteins in vitro and in vivo can be achieved by studying planktonic and different growth phases of biofilms using a proteome analysis approach. Our goal was to construct a reference map of planktonic and biofilm associated proteins of S. aureus. Methods: S. aureus reference strain (ATCC 25923) was used to grow 24 hours planktonic, 3-day wet biofilm (3DWB), and 12-day wet biofilm (12DWB). Bacteria were grown in tryptic soy broth (TSB) liquid medium. Planktonic growth was used late logarithmic bacteria, and the Centres for Disease Control (CDC) biofilm reactor was used to grow 3 days, and 12-day hydrated biofilms, respectively. Samples were subjected to reduction, alkylation and digestion steps prior to Multiplex labelling using Tandem Mass Tag (TMT) 10-plex reagent (Thermo Fisher Scientific). The labelled samples were pooled and fractionated by high pH RP-HPLC which followed by loading of the fractions on a nanoflow UPLC system (Eksigent UPLC system, AB SCIEX). Mass spectrometry (MS) data were collected on an Orbitrap Elite (Thermo Fisher Scientific) Mass Spectrometer. Protein identification and relative quantitation of protein levels were performed using Proteome Discoverer (version 1.3, Thermo Fisher Scientific). After the extraction of protein ratios with Proteome Discoverer, additional processing, and statistical analysis was done using the TMTPrePro R package. Results and Discussion: The present study showed that a considerable proteomic difference exists among planktonic and biofilms from S. aureus. We identified 1636 total extracellular secreted proteins, of which 350 and 137 proteins of 3DWB and 12DWB showed significant abundance variation from planktonic preparation, respectively. Of these, simultaneous up-regulation in between 3DWB and 12DWB proteins such as extracellular matrix-binding protein ebh, enolase, transketolase, triosephosphate isomerase, chaperonin, peptidase, pyruvate kinase, hydrolase, aminotransferase, ribosomal protein, acetyl-CoA acetyltransferase, DNA gyrase subunit A, glycine glycyltransferase and others we found in this biofilm producer. On the contrary, simultaneous down-regulation in between 3DWB and 12DWB proteins such as alpha and delta-hemolysin, lipoteichoic acid synthase, enterotoxin I, serine protease, lipase, clumping factor B, regulatory protein Spx, phosphoglucomutase, and others also we found in this biofilm producer. In addition, we also identified a big percentage of hypothetical proteins including unique proteins. Therefore, a comprehensive knowledge of planktonic and biofilm associated proteins identified by S. aureus will provide a basis for future studies on the development of vaccines and diagnostic biomarkers. Conclusions: In this study, we constructed an initial reference map of planktonic and various growth phase of biofilm associated proteins which might be helpful to diagnose biofilm associated infections.

Keywords: Mass Spectrometry, Bacterial Biofilms, S. aureus, TMT, CDC bioreactor

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9 Glycan Analyzer: Software to Annotate Glycan Structures from Exoglycosidase Experiments

Authors: Ian Walsh, Terry Nguyen-Khuong, Christopher H. Taron, Pauline M. Rudd

Abstract:

Glycoproteins and their covalently bonded glycans play critical roles in the immune system, cell communication, disease and disease prognosis. Ultra performance liquid chromatography (UPLC) coupled with mass spectrometry is conventionally used to qualitatively and quantitatively characterise glycan structures in a given sample. Exoglycosidases are enzymes that catalyze sequential removal of monosaccharides from the non-reducing end of glycans. They naturally have specificity for a particular type of sugar, its stereochemistry (α or β anomer) and its position of attachment to an adjacent sugar on the glycan. Thus, monitoring the peak movements (both in the UPLC and MS1) after application of exoglycosidases provides a unique and effective way to annotate sugars with high detail - i.e. differentiating positional and linkage isomers. Manual annotation of an exoglycosidase experiment is difficult and time consuming. As such, with increasing sample complexity and the number of exoglycosidases, the analysis could result in manually interpreting hundreds of peak movements. Recently, we have implemented pattern recognition software for automated interpretation of UPLC-MS1 exoglycosidase digestions. In this work, we explain the software, indicate how much time it will save and provide example usage showing the annotation of positional and linkage isomers in Immunoglobulin G, apolipoprotein J, and simple glycan standards.

Keywords: Bioinformatics, Mass Spectrometry, liquid chromatography, automated glycan assignment

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8 High Throughput LC-MS/MS Studies on Sperm Proteome of Malnad Gidda (Bos Indicus) Cattle

Authors: Manish Kumar, Kerekoppa Puttaiah Bhatta Ramesha, Uday Kannegundla, Praseeda Mol, Lathika Gopalakrishnan, Jagish Kour Reen, Gourav Dey, Sakthivel Jeyakumar, Arumugam Kumaresan, Kiran Kumar M., Thottethodi Subrahmanya Keshava Prasad

Abstract:

Spermatozoa are the highly specialized transcriptionally and translationally inactive haploid male gamete. The understanding of proteome of sperm is indispensable to explore the mechanism of sperm motility and fertility. Though there is a large number of human sperm proteomic studies, in-depth proteomic information on Bos indicus spermatozoa is not well established yet. Therefore, we illustrated the profile of sperm proteome in indigenous cattle, Malnad gidda (Bos Indicus), using high-resolution mass spectrometry. In the current study, two semen ejaculates from 3 breeding bulls were collected employing the artificial vaginal method. Using 45% percoll purification, spermatozoa cells were isolated. Protein was extracted using lysis buffer containing 2% Sodium Dodecyl Sulphate (SDS) and protein concentration was estimated. Fifty micrograms of protein from each individual were pooled for further downstream processing. Pooled sample was fractionated using SDS-Poly Acrylamide Gel Electrophoresis, which is followed by in-gel digestion. The peptides were subjected to C18 Stage Tip clean-up and analyzed in Orbitrap Fusion Tribrid mass spectrometer interfaced with Proxeon Easy-nano LC II system (Thermo Scientific, Bremen, Germany). We identified a total of 6773 peptides with 28426 peptide spectral matches, which belonged to 1081 proteins. Gene ontology analysis has been carried out to determine the biological processes, molecular functions and cellular components associated with sperm protein. The biological process chiefly represented our data is an oxidation-reduction process (5%), spermatogenesis (2.5%) and spermatid development (1.4%). The highlighted molecular functions are ATP, and GTP binding (14%) and the prominent cellular components most observed in our data were nuclear membrane (1.5%), acrosomal vesicle (1.4%), and motile cilium (1.3%). Seventeen percent of sperm proteins identified in this study were involved in metabolic pathways. To the best of our knowledge, this data represents the first total sperm proteome from indigenous cattle, Malnad Gidda. We believe that our preliminary findings could provide a strong base for the future understanding of bovine sperm proteomics.

Keywords: Mass Spectrometry, spermatozoa, Bos indicus, Malnad Gidda

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7 Accelerator Mass Spectrometry Analysis of Isotopes of Plutonium in PM₂.₅

Authors: C. G. Mendez-Garcia, E. T. Romero-Guzman, H. Hernandez-Mendoza, C. Solis, E. Chavez-Lomeli, E. Chamizo, R. Garcia-Tenorio

Abstract:

Plutonium is present in different concentrations in the environment and biological samples related to nuclear weapons testing, nuclear waste recycling and accidental discharges of nuclear plants. This radioisotope is considered the most radiotoxic substance, particularly when it enters the human body through inhalation of powders insoluble or aerosols. This is the main reason of the determination of the concentration of this radioisotope in the atmosphere. Besides that, the isotopic ratio of ²⁴⁰Pu/²³⁹Pu provides information about the origin of the source. PM₂.₅ sampling was carried out in the Metropolitan Zone of the Valley of Mexico (MZVM) from February 18th to March 17th in 2015 on quartz filter. There have been significant developments recently due to the establishment of new methods for sample preparation and accurate measurement to detect ultra trace levels as the plutonium is found in the environment. The accelerator mass spectrometry (AMS) is a technique that allows measuring levels of detection around of femtograms (10-15 g). The AMS determinations include the chemical isolation of Pu. The Pu separation involved an acidic digestion and a radiochemical purification using an anion exchange resin. Finally, the source is prepared, when Pu is pressed in the corresponding cathodes. According to the author's knowledge on these aerosols showed variations on the ²³⁵U/²³⁸U ratio of the natural value, suggesting that could be an anthropogenic source altering it. The determination of the concentration of the isotopes of Pu can be a useful tool in order the clarify this presence in the atmosphere. The first results showed a mean value of activity concentration of ²³⁹Pu of 280 nBq m⁻³ thus the ²⁴⁰Pu/²³⁹Pu was 0.025 corresponding to the weapon production source; these results corroborate that there is an anthropogenic influence that is increasing the concentration of radioactive material in PM₂.₅. According to the author's knowledge in Total Suspended Particles (TSP) have been reported activity concentrations of ²³⁹⁺²⁴⁰Pu around few tens of nBq m⁻³ and 0.17 of ²⁴⁰Pu/²³⁹Pu ratios. The preliminary results in MZVM show high activity concentrations of isotopes of Pu (40 and 700 nBq m⁻³) and low ²⁴⁰Pu/²³⁹Pu ratio than reported. These results are in the order of the activity concentrations of Pu in weapons-grade of high purity.

Keywords: Aerosols, Radiochemistry, Mass Spectrometry, tracer, fallout, ²⁴⁰Pu/²³⁹Pu ratio

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6 N-Glycosylation in the Green Microalgae Chlamydomonas reinhardtii

Authors: Pierre-Louis Lucas, Corinne Loutelier-Bourhis, Narimane Mati-Baouche, Philippe Chan Tchi-Song, Patrice Lerouge, Elodie Mathieu-Rivet, Muriel Bardor

Abstract:

N-glycosylation is a post-translational modification taking place in the Endoplasmic Reticulum and the Golgi apparatus where defined glycan features are added on protein in a very specific sequence Asn-X-Thr/Ser/Cys were X can be any amino acid except proline. Because it is well-established that those N-glycans play a critical role in protein biological activity, protein half-life and that a different N-glycan structure may induce an immune response, they are very important in Biopharmaceuticals which are mainly glycoproteins bearing N-glycans. From now, most of the biopharmaceuticals are produced by mammalian cells like Chinese Hamster Ovary cells (CHO) for their N-glycosylation similar to the human, but due to the high production costs, several other species are investigated as the possible alternative system. In this purpose, the green microalgae Chlamydomonas reinhardtii was investigated as the potential production system for Biopharmaceuticals. This choice was influenced by the facts that C. reinhardtii is a well-study microalgae which is growing fast with a lot of molecular biology tools available. This organism is also producing N-glycan on its endogenous proteins. However, the analysis of the N-glycan structure of this microalgae has revealed some differences as compared to the human. Rather than in Human where the glycans are processed by key enzymes called N-acetylglucosaminyltransferase I and II (GnTI and GnTII) adding GlcNAc residue to form a GlcNAc₂Man₃GlcNAc₂ core N-glycan, C. reinhardtii lacks those two enzymes and possess a GnTI independent glycosylation pathway. Moreover, some enzymes like xylosyltransferases and methyltransferases not present in human are supposed to act on the glycans of C. reinhardtii. Furthermore, the recent structural study by mass spectrometry shows that the N-glycosylation precursor supposed to be conserved in almost all eukaryotic cells results in a linear Man₅GlcNAc₂ rather than a branched one in C. reinhardtii. In this work, we will discuss the new released MS information upon C. reinhardtii N-glycan structure and their impact on our attempt to modify the glycan in a Human manner. Two strategies will be discussed. The first one consisted in the study of Xylosyltransferase insertional mutants from the CLIP library in order to remove xyloses from the N-glycans. The second will go further in the humanization by transforming the microalgae with the exogenous gene from Toxoplasma gondii having an activity similar to GnTI and GnTII with the aim to synthesize GlcNAc₂Man₃GlcNAc₂ in C. reinhardtii.

Keywords: Mass Spectrometry, Chlamydomonas reinhardtii, humanization, N-glycosylation, glycosyltransferase

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5 Plasmonic Nanoshells Based Metabolite Detection for in-vitro Metabolic Diagnostics and Therapeutic Evaluation

Authors: Deepanjali Gurav, Kun Qian

Abstract:

In-vitro metabolic diagnosis relies on designed materials-based analytical platforms for detection of selected metabolites in biological samples, which has a key role in disease detection and therapeutic evaluation in clinics. However, the basic challenge deals with developing a simple approach for metabolic analysis in bio-samples with high sample complexity and low molecular abundance. In this work, we report a designer plasmonic nanoshells based platform for direct detection of small metabolites in clinical samples for in-vitro metabolic diagnostics. We first synthesized a series of plasmonic core-shell particles with tunable nanoshell structures. The optimized plasmonic nanoshells as new matrices allowed fast, multiplex, sensitive, and selective LDI MS (Laser desorption/ionization mass spectrometry) detection of small metabolites in 0.5 μL of bio-fluids without enrichment or purification. Furthermore, coupling with isotopic quantification of selected metabolites, we demonstrated the use of these plasmonic nanoshells for disease detection and therapeutic evaluation in clinics. For disease detection, we identified patients with postoperative brain infection through glucose quantitation and daily monitoring by cerebrospinal fluid (CSF) analysis. For therapeutic evaluation, we investigated drug distribution in blood and CSF systems and validated the function and permeability of blood-brain/CSF-barriers, during therapeutic treatment of patients with cerebral edema for pharmacokinetic study. Our work sheds light on the design of materials for high-performance metabolic analysis and precision diagnostics in real cases.

Keywords: Mass Spectrometry, Fingerprinting, Metabolites, Plasmonic Nanoparticles, in-vitro diagnostics

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4 A Plasmonic Mass Spectrometry Approach for Detection of Small Nutrients and Toxins

Authors: Kun Qian, Haiyang Su

Abstract:

We developed a novel plasmonic matrix assisted laser desorption/ionization mass spectrometry (MALDI MS) approach to detect small nutrients and toxin in complex biological emulsion samples. We used silver nanoshells (SiO₂@Ag) with optimized structures as matrices and achieved direct analysis of ~6 nL of human breast milk without any enrichment or separation. We performed identification and quantitation of small nutrients and toxins with limit-of-detection down to 0.4 pmol (for melamine) and reaction time shortened to minutes, superior to the conventional biochemical methods currently in use. Our approach contributed to the near-future application of MALDI MS in a broad field and personalized design of plasmonic materials for real case bio-analysis.

Keywords: Toxins, Mass Spectrometry, plasmonic materials, laser desorption/ionization, small nutrients

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3 Persistent Ribosomal In-Frame Mis-Translation of Stop Codons as Amino Acids in Multiple Open Reading Frames of a Human Long Non-Coding RNA

Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

Abstract:

Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: Mass Spectrometry, Ribosome, proteogenomics, RNAseq, LncRNA, genetic code, long non-coding RNA, ribo-seq

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2 Staphylococcus argenteus: An Emerging Subclinical Bovine Mastitis Pathogen in Thailand

Authors: Natapol Pumipuntu

Abstract:

Staphylococcus argenteus is the emerging species of S. aureus complex. It was generally misidentified as S. aureus by standard techniques and their features. S. argenteus is possibly emerging in both humans and animals, as well as increasing worldwide distribution. The objective of this study was to differentiate and identify S. argenteus from S. aureus, which has been collected and isolated from milk samples of subclinical bovine mastitis cases in Maha Sarakham province, Northeastern of Thailand. Twenty-one isolates of S. aureus, which confirmed by conventional methods and immune-agglutination method were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and multilocus sequence typing (MLST). The result from MALDI-TOF MS and MLST showed 6 from 42 isolates were confirmed as S. argenteus, and 36 isolates were S. aureus, respectively. This study indicated that the identification and classification method by using MALDI-TOF MS and MLST could accurately differentiate the emerging species, S. argenteus, from S. aureus complex which usually misdiagnosed. In addition, the identification of S. argenteus seems to be very limited despite the fact that it may be the important causative pathogen in bovine mastitis as well as pathogenic bacteria in food and milk. Therefore, it is very necessary for both bovine medicine and veterinary public health to emphasize and recognize this bacterial pathogen as the emerging disease of Staphylococcal bacteria and need further study about S. argenteus infection.

Keywords: Mass Spectrometry, MLST, Staphylococcus argenteus, subclinical bovine mastitis, Staphylococcus aureus complex

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1 Identification of Salt Responsive Proteins in Rice Leaf Sheath (Oryza sativa L.) with Nanoliquid Chromatography-Tandem Mass Spectrometry

Authors: Kanlaya Kong-ngern, Sittiruk Roytrakul, Chutima Homwonk

Abstract:

In this research, we compared the proteomic profile of two rice leaf sheaths under salt stress, Thai moderately salt tolerant rice (Leaung Anan), and high salt tolerant rice (Pokkali). Seeds were grown in hydroponic culture for 21 days before NaCl was introduced initially at the level of 12 dS m⁻¹ for 10 days. Then the leaf sheath proteomes were analyzed by 1D-SDS-PAGE and NanoLC-MS/MS. In this study, 873 proteins were detected. Among these proteins, 219 proteins were known proteins and the other proteins were unnamed and unknown proteins. By using Mev software, we found that only 31 proteins in treated plants of both rice cultivars significantly expressed, 21 proteins were up-regulated and 10 proteins were down-regulated. Interestingly, the intensity of the 3 proteins in the Leaung Anan more expressed than in the Pokkali. The results indicate that the up-regulated proteins were more expressed in less tolerant rice may play an important role in helping rice to survive under salt stress.

Keywords: Proteomics, Mass Spectrometry, Salt Stress, rice leaf sheaths

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