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Relevant bibliographies by topics / Comprehensive proteomics

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Academic literature on the topic 'Comprehensive proteomics'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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Journal articles on the topic "Comprehensive proteomics"

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Beck, Martin, Manfred Claassen, and Ruedi Aebersold. "Comprehensive proteomics." Current Opinion in Biotechnology 22, no. 1 (February 2011): 3–8. http://dx.doi.org/10.1016/j.copbio.2010.09.002.

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Donato, P., F. Cacciola, L. Mondello, and P. Dugo. "Comprehensive chromatographic separations in proteomics." Journal of Chromatography A 1218, no. 49 (December 2011): 8777–90. http://dx.doi.org/10.1016/j.chroma.2011.05.070.

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Ji, Qing, Fangshi Zhu, Xuan Liu, Qi Li, and Shi-bing Su. "Recent Advance in Applications of Proteomics Technologies on Traditional Chinese Medicine Research." Evidence-Based Complementary and Alternative Medicine 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/983139.

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Proteomics technology, a major component of system biology, has gained comprehensive attention in the area of medical diagnosis, drug development, and mechanism research. On the holistic and systemic theory, proteomics has a convergence with traditional Chinese medicine (TCM). In this review, we discussed the applications of proteomic technologies in diseases-TCM syndrome combination researches. We also introduced the proteomic studies on thein vivoandin vitroeffects and underlying mechanisms of TCM treatments using Chinese herbal medicine (CHM), Chinese herbal formula (CHF), and acupuncture. Furthermore, the combined studies of proteomics with other “-omics” technologies in TCM were also discussed. In summary, this report presents an overview of the recent advances in the application of proteomic technologies in TCM studies and sheds a light on the future global and further research on TCM.

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Avram, Oren, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, and Yariv Wine. "PASA: Proteomic analysis of serum antibodies web server." PLOS Computational Biology 17, no. 1 (January 25, 2021): e1008607. http://dx.doi.org/10.1371/journal.pcbi.1008607.

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Motivation A comprehensive characterization of the humoral response towards a specific antigen requires quantification of the B-cell receptor repertoire by next-generation sequencing (BCR-Seq), as well as the analysis of serum antibodies against this antigen, using proteomics. The proteomic analysis is challenging since it necessitates the mapping of antigen-specific peptides to individual B-cell clones. Results The PASA web server provides a robust computational platform for the analysis and integration of data obtained from proteomics of serum antibodies. PASA maps peptides derived from antibodies raised against a specific antigen to corresponding antibody sequences. It then analyzes and integrates proteomics and BCR-Seq data, thus providing a comprehensive characterization of the humoral response. The PASA web server is freely available at https://pasa.tau.ac.il and open to all users without a login requirement.

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Masood, Afshan, Hicham Benabdelkamel, and Assim Alfadda. "Obesity Proteomics: An Update on the Strategies and Tools Employed in the Study of Human Obesity." High-Throughput 7, no. 3 (September 12, 2018): 27. http://dx.doi.org/10.3390/ht7030027.

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Proteomics has become one of the most important disciplines for characterizing cellular protein composition, building functional linkages between protein molecules, and providing insight into the mechanisms of biological processes in a high-throughput manner. Mass spectrometry-based proteomic advances have made it possible to study human diseases, including obesity, through the identification and biochemical characterization of alterations in proteins that are associated with it and its comorbidities. A sizeable number of proteomic studies have used the combination of large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography in combination with mass spectrometry, for high-throughput protein identification. These studies have applied proteomics to comprehensive biochemical profiling and comparison studies while using different tissues and biological fluids from patients to demonstrate the physiological or pathological adaptations within their proteomes. Further investigations into these proteome-wide alterations will enable us to not only understand the disease pathophysiology, but also to determine signature proteins that can serve as biomarkers for obesity and related diseases. This review examines the different proteomic techniques used to study human obesity and discusses its successful applications along with its technical limitations.

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Jenkins, Conor, and Benjamin Orsburn. "The Cannabis Proteome Draft Map Project." International Journal of Molecular Sciences 21, no. 3 (January 31, 2020): 965. http://dx.doi.org/10.3390/ijms21030965.

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Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources developed from our proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources.

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Baker, M. S., P. Haynes, A. Len, M. Molloy, A. Lee, R. Saldanha, and J. Chick. "Desperately Seeking Comprehensive Mammalian Membrane Proteomics." Journal of Proteomics & Bioinformatics S2, no. 01 (July 2008): 108–9. http://dx.doi.org/10.4172/jpb.s1000088.

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Dunn, Michael J. "PROTEOMICS - Continued growth and comprehensive coverage." PROTEOMICS 6, no. 1 (January 2006): 1–3. http://dx.doi.org/10.1002/pmic.200690000.

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Hendriks, Ivo A., and Alfred C. O. Vertegaal. "A comprehensive compilation of SUMO proteomics." Nature Reviews Molecular Cell Biology 17, no. 9 (July 20, 2016): 581–95. http://dx.doi.org/10.1038/nrm.2016.81.

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Mirza, Shama P., and Michael Olivier. "Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry." Physiological Genomics 33, no. 1 (March 2008): 3–11. http://dx.doi.org/10.1152/physiolgenomics.00292.2007.

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Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins.

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Dissertations / Theses on the topic "Comprehensive proteomics"

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Munshi, Afnan M. N. Alam. "Comprehensive Proteomic Analysis and Characterization of Human Bone Marrow Mesenchymal Stem/Stromal Derived Extracellular Vesicles." Thesis, Université d'Ottawa / University of Ottawa, 2019. http://hdl.handle.net/10393/39538.

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Goldberger, Natalie Elizabeth. "A comprehensive investigation into the molecular mechanism responsible for selective androgen receptor (SARM) tissue-selectivity." Columbus, Ohio : Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1202342545.

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Mehta, Virja. "A Comprehensive Analysis of PP1c Leads to the Identification and Characterization of a Novel Family of Regulators for the Mypt1/PP1β Phosphatase." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/36465.

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Reversible protein phosphorylation, the best studied post-translational modification, regulates most cellular processes, including signaling, migration, cell cycle progression, DNA damage repair, stress response and modulaton of the activities of metabolic enzymes. Therefore, it has emerged as a key therapeutic target in diseases in which these processes are deregulated. Unlike kinases, protein phosphatase 1 (PP1) is a promiscuous enzyme that gains its substrate specificity from a large group of “regulatory subunits” with which it associates to form a range of holoenzyme complexes targeted to specific subcellular localizations and substrates. Inhibition of a specific dephosphorylation event therefore relies on targeting the regulatory rather than the catalytic subunit. The present study uses GFP as a molecular reporter to assess the localization of PP1c and identify the underlying binding events that govern it via a combination of fluorescence imaging, cellular fractionation, affinity purification and quantitative mass spectrometry. While there is some overlap in their targeting and intracellular roles, the three PP1 isoforms show distinct localizations based on relative preferences for particular regulatory subunits. In this study we assembled a comprehensive map of isoform- and compartment- specific phosphatase complexes in three different cultured human cell lines, using the data to extrapolate, with confidence, the distribution of each PP1 isoform between a large pool of known/predicted and novel regulatory subunits. Network analysis also highlighted key multiprotein complexes to which PP1 is targeted by these regulatory subunits, and identified a novel regulatory subunit that links phosphatase activity to regulation of protein degradation. Our work confirmed that Mypt1, the regulatory subunit that targets PP1 activity to the myosin light chain, preferentially associates with the beta isoform of PP1c. We further demonstrated that they are in complex in both the cytoplasm and nucleus, and represent ~30% of the total PP1β holoenzyme complexes in both interaphase and mitotic cells. Further investigation of these complexes led to the discovery of Specc1 and Specc1L, which associate with Mypt1/PP1β via direct binding to Mypt1. Specc1/1L are microtubule binding proteins that can also associate with actin filaments, and we demonstrated that they mediate the distribution of Mypt1/PP1β complexes between these two cytoskeletal networks. Given that disruption of this balance has been implicated in disease states including cancer and hypertension, the Specc1/L family represents a novel therapeutic target for the regulation of Mypt1/PP1 activity. With PP1 now emerging as a promising therapeutic target and the first PP1-targeted therapeutic drug, Sephin 1, in clinical trials, a better understanding of PP1’s in vivo distribution between holoenzyme complexes is essential. Our work establishes an initial “snapshot” of this distribution against which changes can be assessed, as we demonstrated here by showing its re-distribution in mitotic cells. Dynamic redistributions during specific cell processes such as differentiation or in response to perturbations or disease states can be assessed in a similar fashion in future, facilitating both identification of the relevant complexes and the design of specific strategies to target them therapeutically.

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Maltman, Daniel James. "Characterization of endoplasmic reticulum from castor bean and the cloning of a plant phosphatase : a basis for comprehensive plant organelle proteomics research." Thesis, Durham University, 2000. http://etheses.dur.ac.uk/4958/.

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The plant endoplasmic reticulum is the location of storage oil and membrane lipid assembly, and for fatty acid modifying reactions (desaturation, elongation, hydroxylation). It therefore represents a source of enzymes involved in these processes. Many of these defy traditional purification strategies. In this study, ER membranes have been isolated biochemically pure and in milligram quanties from the endosperm of developing and germinating castor bean. One-dimensional SDS- PAGE, used to routinely assess sample integrity, showed resolution limitations. Two-dimensional gel electrophoresis was optimized regarding sample preparation and solubilization, and reproducible profiles confirmed its suitability as a sound basis for analysis of stage-specific ER components. In large format 2-D experiments, preparative loadings were reproducibly resolved. MALDI TOP mass spectrometry was evaluated for high throughput peptide signature generation with individual ER components. Resolution problems were again highlighted with 1-D separations, although some functional assignments were made. Subsequently analysis of selected spots from a preparative 2-D gel of germinating ER was used to establish the limitations of the procedure. Database matching of a single component at very low levels of mass error tolerance also demonstrated the power and accuracy of the technology. Membranes were subfractionated to simplify protein patterns. It is proposed that an organellar approach, including subfractionation, provides enrichment of specific subsets of cellular components. A putative plant phosphatidic acid phosphatase gene has been investigated following identification from the EST database. The aim of this research is the identification of proteins involved in storage lipid synthesis in castor bean in reactions specific to the endoplasmic reticulum.

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Kierul, Kinga. "Comprehensive proteomic study of Bacillus amyloliquefaciens strain FZB42 and its response to plant root exudates." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2013. http://dx.doi.org/10.18452/16805.

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Bacillus amyloliquefaciens FZB42 ist ein frei lebendes Bakterium, das Pflanzenwurzeln besiedelt und das Pflanzenwachstum durch viele verschiedene Wirkmechanismen anregt. In dieser Arbeit wurden die molekularen Grundlagen dieser positiven Wirkungen, die dieses „Pflanzenwachstum fördernde Rhizobakterium“ (PGPR) auf seine Wirte ausübt, untersucht. Um den gegenseitigen Austausch von B. amyloliquefaciens und seinen Wirtspflanzen zu entschlüsseln, wurden umfangreiche Proteomstudien durchgeführt. Es wurden Referenzkarten der extrazellulären und zytosolischen Proteinfraktionen erstellt. Die größte Anzahl an ausgeschiedenen Proteinen konnte während der stationären Phase beobachtet werden. Die identifizierten extrazellulären Proteine gehören verschiedenen Funktionsklassen an, wobei die prominentesten Klassen am Kohlenhydrat-Abbau und den Transport von Molekülen durch die Zellwand beteiligt sind. Die zytosolischen Extrakte von Kulturen, die in 1C-Medium bzw. Mineralmedium angezogen wurden, und in der zweidimensionalen Gelelektrophorese (2 DE) aufgetrennt wurden, ergaben 461 und 245 verschiedene Protein-Einträge. Die erstellten Referenz-Karten wurden anschließend verwendet, um Proteine und Prozesse, in an der Interaktion mit Pflanzen beteiligt sind, zu identifizieren. Dafür wurden die Bakterien Wurzelexudaten von Mais (Zea mays L.) ausgesetzt. Die Proteine aus zwei Stämmen, denen die globalen Transkriptionsregulatoren (Degu, AbrB) und vier Sigma-Faktoren (SigB, SigM, SigV, und SigX) fehlen, wurden ebenfalls untersucht, um ihre Beteiligung an den bakteriellen Reaktionen auf die Wurzelausscheidungen zu analysieren. Zusammenfassend ist dies die erste Studie, die umfangreiche Proteomdaten von Gram-positiven PGPR präsentiert, wobei gleichzeitig die Veränderung der Expression von extrazellulären und zytoplasmatischen Proteinen, nach Zugabe von Wurzelexudaten, ausgewertet wurde.
Bacillus amyloliquefaciens strain FZB42 is a free-living bacterium that competitively colonizes plant roots and stimulates plant growth by many different modes of action. The molecular basis of singular beneficial effects that this Plant Growth-Promoting Rhizobacteria (PGPR) exert on their hosts have been studied. To decipher the molecular cross-talk of B. amyloliquefaciens and its’ host plants as a whole system, an extensive proteomic approach was performed. Reference maps of the extracellular and cytosolic protein fractions were established. The highest number of secreted proteins was observed during stationary growth phase. Identified extracellular proteins belong to different functional classes, with the most prominent classes involved in carbohydrate degradation and transportation of molecules across the cell wall. Cytosolic extracts obtained from cultures grown in 1C and minimal media subjected to the 2 Dimensional Electrophoresis (2 DE), revealed 461 and 245 different protein entries, respectively. Created reference maps were subsequently used to identify proteins and processes involved in the interaction with plants, prior to exposure of bacteria to maize (Zea mays L.) root exudates. The proteomics of two strains lacking expression of genes coding for global transcriptional regulators (degU, abrB) and four sigma factors (sigB, sigM, sigV, and sigX) were also inves-tigated, in order to analyse their involvement in bacterial responses to root exudates. In summary, this is the first study presenting comprehensive proteomics of Gram-positive PGPR, evaluating at the same time changes in protein expression caused by addition of root exudates at the extracellular and cytosolic level.

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Hezinová, Věra. "Vývoj instrumentace a metodiky v proteomické a environmentální analýze." Doctoral thesis, Vysoké učení technické v Brně. Fakulta chemická, 2011. http://www.nusl.cz/ntk/nusl-233327.

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Tato práce je zaměřena jak na cílený tak na přehledný přístup ve studiu proteomiky. Cílená proteomika přináší informace o přítomnosti proteinu a jeho lokalizaci v buňce či tkáni pomocí luminiscenčních značek na bázi kvantových teček, zatímco přehledná proteomika se zabývá identifikací změn v proteomu dvou nebo více jedinců stejného druhu vystavených různým podmínkám. Protože proteomika vyžaduje vysoce citlivé separační a identifikační techniky, byly v této práci ověřeny různé metody zlepšení citlivosti kapilární elektroforézy s hmotnostní detekcí. Použití rozhraní s kapalinovým spojem pro spojení těchto dvou technik, které zajišťuje vyšší citlivost analýz, bylo také ověřeno analýzou metabolitů etanolu a kokainu v lidské moči. Zavedené techniky instrumentace jsou využitelné při posouzení vlivu významných faktorů životního prostředí na živé systémy jak na buněčné tak na molekulární úrovni.

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Simon, Coma Marina. "Comprehensive Molecular Characterization of Childhood Liver Cancer: Identification of Prognostic Biomarkers." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/664344.

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Malignant tumors in children and adolescents are one of the leading causes of death from disease in this population despite being rare events. The main liver tumor in children is Hepatoblastoma (HB) representing two thirds of the total while pediatric Hepatocellular Carcinoma (pHCC) is rarer than HB and is usually diagnosed in older patients. Patient survival at 5 years is higher than 75% for HB and less than 30% for pHCC. At molecular level, 2 different subclasses of HBs have been described based on a 16-gene signature, C1 and C2, being the latest more aggressive. Nowadays patient stratification is based only in clinical and pathological parameters. For this reason, the identification of prognostic markers easy to apply at the clinical practice is mandatory in order to better stratify patients and diminish the side effects of chemotherapy treatment, moving towards a more personalized medicine. The proteomic profile of 16HBs and 8 paired normal liver (NL) tissue was obtained by 2 different techniques, two-dimensional gel electrophoresis and label-free LC-MS. The differential expressed proteins were validated by western blot (WB) in the same patients and the final protein signature was validated by immunohistochemistry in additional 144 patients. Furthermore, RNA sequencing and copy number variation analysis were performed in 31 HB samples, 11 patient-derived xenografts (PDXs) and 5 pHCC. Results were validated by Sanger sequencing, droplet digital PCR or real time PCR and correlated with clinical features. Two hundred and thirty proteins were identified as deregulated in aggressive C2 tumors and 8 of them were selected and validated by WB considering also their expression in NL. After WB, 2 proteins were found significantly upregulated in C2 tumors while 1 was downregulated. A score was calculated for each protein and biomarkers 1 and 2 were considered altered when their staining was at least 2-fold higher than the NL while the biomarker 3 was considered as altered when no staining was observed. The 3-protein signature was defined by the number of altered biomarkers in each tumor and was highly correlated with patient survival and complementary to the current clinical stratification. RNA-sequencing data revealed that fusion proteins are rare events in HB as they were found in only 2% of patients. Mutational analysis allowed us to identify mutations in CTNNB1 (30%), NFE2L2 (7%) and EPHB4 (7%). Interestingly we identified a downregulation of the RNA editing which is correlated with patient outcome. The copy number variation analysis showed that gains are more frequent than losses in HB tumors and that PDXs maintain 78% of the aberrations, being a good model for the study of HB. In contrast, pHCC are characterized by more aberrations than HB and mainly losses. Thus, we stablished a molecular classification that includes 3 HB types: stable (no big CNVs), gains-enriched and losses-enriched classes. This classification is correlated with event-free survival, CTNNB1 mutations and the expression of stem cell markers. As a result of this thesis, we stablished a 3-protein signature that could be easily applied at the clinical practice and increased the molecular knowledge of childhood liver tumors.
Els tumors malignes en nens i adolescents són una de les principals causes de mort per malaltia en aquesta població malgrat ser poc freqüents. El principal tumor de fetge en la infància és l’Hepatoblastoma (HB) mentre que el Carcinoma Hepatocel·lular pediàtric (pHCC) és menys freqüent i normalment es diagnostica en pacients més grans. La supervivència als 5 anys és superior al 75% per l’HB i menor del 30% pel pHCC. A nivell molecular, s’han descrit 2 subclasses d’HB en base a una signatura de 16 gens, C1 i C2, essent la segona més agressiva. Actualment l’estratificació dels pacients es basa només en paràmetres clínics i patològics. Per aquesta raó, la identificació de marcadors pronòstic que siguin fàcilment aplicables a la pràctica clínica és imprescindible per a una millor estratificació els pacients per tal de disminuir els efectes secundaris de la quimioteràpia, avançant cap a una medicina personalitzada. Es va estudiar el perfil proteòmic de 16 HBs i 8 teixits no tumorals (NL) mitjançant 2 tècniques, l’electroforesi bidimensional amb fluorescència i una tècnica sense marcatge LC-MS. Les proteïnes amb expressió diferencial es van validar per western blot (WB) en els mateixos pacients i la signatura final es va validar per immunohistoquímica en 144 pacients. A més, es va realitzar seqüenciació de RNA i un array genòmic en 31HBs, 11 xenògrafts derivats de pacients (PDXs) i 5 pHCC. Els resultats es van validar per seqüenciació Sanger, droplet digital PCR o PCR a temps real i correlacionar amb característiques clíniques. Es van identificar 230 proteïnes desregulades en els tumors agressius C2 i 8 d’aquestes es van seleccionar per ser validades per WB considerant també la seva expressió en NL. Els resultats del WB van confirmar que 2 de les proteïnes estaven sobreexpressades en els tumors C2 mentre que una d’elles estava infraexpressada. Es va calcular una puntuació per cada proteïna, de manera que els biomarcadors 1 i 2 es consideren desregulats si la seva expressió és superior a 2 vegades l’expressió del NL mentre que BM3 es considera alterat si no es detecta expressió. La firma de 3 proteïnes, que es va definir com el número de biomarcadors alterats, estava fortament correlacionada amb la supervivència i era complementària a l’actual estratificació clínica. Les dades de seqüenciació de RNA van revelar que les proteïnes de fusió són poc freqüents en HB i l’anàlisi de mutacions ens va permetre identificar mutacions en CTNNB1 (30%), NFE2L2 (7%) i EPHB4 (7%). A més, vam identificar una infra-regulació del mecanisme d’edició del RNA correlacionat amb el pronòstic. L’anàlisi genòmic va mostrar que els guanys cromosòmics són més freqüents que les pèrdues en l’HB i que els PDXs mantenen un 78% de les alteracions, representant un bon model per a l’estudi del HB. Per contra, el pHCC presenta més alteracions que l’HB i majoritàriament pèrdues. Finalment, vam establir una classificació molecular que inclou 3 classes d’HB: estable, enriquida en guanys i enriquida en pèrdues. Aquesta classificació està correlacionada amb la supervivència, mutacions de CTNNB1 i expressió de marcadors de cèl·lules progenitores. Amb aquesta tesi, hem establert una signatura de 3 proteïnes fàcilment aplicable a la pràctica clínica i augmentat el coneixement molecular dels tumors hepàtics pediàtrics.

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Rohrbough, James Gary Jr. "Identification of Protein Vaccine Candidates Using Comprehensive Proteomic Analysis Strategies." Diss., The University of Arizona, 2007. http://hdl.handle.net/10150/194491.

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Presented in this dissertation are proteomic analysis studies focused on identifying proteins to be used as vaccine candidates against Coccidioidomycosis, a potentially fatal human pulmonary disease caused by inhalation of a spore from the soil-dwelling pathogenic fungi Coccidioides posadasii and C. immitis. A method of tandem mass spectrometry data analysis using dual protein sequence search algorithms for increasing the total protein identifications from an analysis is described. This method was utilized in a comprehensive proteomic analysis of cell walls isolated from the dimorphic fungal pathogen C. posadasii. A strategy of tandem mass spectrometry-based protein identification coupled with bioinformatic sequence analysis was used to produce a list of protein vaccine candidates for further testing. A differential proteome analysis using stable isotope protein labeling was undertaken to identify vaccine candidate proteins that are more highly expressed in the spherule, or pathogenic phase, of C. posadasii. The results of these analyses are 9 previously undescribed protein vaccine candidates isolated from spherule cell walls that have sequence indications of extracellular association such as GPI anchors and N-terminal signal sequences and antigen potential based on homology to known antigenic or secreted proteins. An additional 14 proteins identified from spherule cell walls are potential vaccine candidates based on extracellular sequence predictions without any indications of antigenic potential. The stable isotope labeling study has identified 3 more proteins that are preferentially expressed in spherules and exhibit antigenic potential based on extracellular localization or homology to known antigenic proteins. Additionally, there were 5 unknown function proteins identified by stable isotope labeling that are more highly expressed in spherules that may be good vaccine candidates but cannot be identified or localized by sequence analysis.The dual algorithm protein identification method presented here is a new technique to address some common shortcomings associated with a proteomic analysis. The comprehensive proteomic analyses of Coccidioides posadasii presented here have provided new targets for Coccidioidomycosis vaccine development as well as insights into the proteome of this pathogen, such as the sequence comparison of C.posadasii proteins to human proteins, as well as a comprehensive analysis of predicted protein function in the Coccidioides proteome.

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Peters, Julian S. "Comprehensive proteomic profiling of clinically relevant strains of Mycobacterium tuberculosis." Doctoral thesis, University of Cape Town, 2014. http://hdl.handle.net/11427/12959.

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Includes bibliographical references.
Tuberculosis is an airborne infectious disease caused by the bacillus known as Mycobacterium tuberculosis. Despite limited genetic variability, Mycobacterium tuberculosis strains exhibit vast discrepancies in phenotypic presentation in terms of virulence, elicited immune response and transmissibility. This study aims to use Mass Spectrometry (MS) tools to quantitatively and qualitatively investigate the total proteome expressed by various epidemiologically significant strains within the Mycobacterium tuberculosis complex (MTBC) as well as a clinically relevant non-tuberculous Mycobacteria (NTM) strain when cultured in vitro. We aim to use the experimental data obtained using discovery mass spectrometry to identify candidate proteins to use in the design of multiple reaction monitoring (MRM) MS experiments for targeted biomarker validation in patient derived biological samples such as sputum. Liquid chromatography mass spectrometry (LC MS/MS) and data capture were carried out using the LTQ Orbitrap Velos. 1D LC was carried out on gel fractionated samples to increase proteome coverage. This allowed a significant increase in the number of protein identifications of up to 80% proteome coverage per strain. Comparative analysis of the datasets was carried out to identify and define the core-proteome expressed across all strains as well as to identify differentially expressed proteins amongst the strains.

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Larracas, Camille V. "COMPREHENSIVE PROTEOMIC ANALYSIS OF DRAGLINE SILK AND MAJOR AMPULLATE GLANDS FROM THE BLACK WIDOW SPIDER, Latrodectus hesperus." Scholarly Commons, 2017. https://scholarlycommons.pacific.edu/uop_etds/3658.

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The outstanding material properties of spider dragline silk fibers have been attributed to two spidroins, MaSp1 and MaSp2. Although dragline silk fibers have been treated with different chemical solvents to elucidate the relationship between protein structure and fiber mechanics, there has not been a comprehensive proteomic analysis of the major ampullate (MA) gland, its spinning dope, and dragline silk using a wide range of chaotropic agents, inorganic salts, and fluorinated alcohols to elucidate their complete molecular constituents. In these studies, we perform in-solution tryptic digestions of solubilized MA glands, spinning dope and dragline silk fibers using 5 different solvents, followed by nanoLC-MS/MS analysis with an Orbitrap Fusion™ Tribrid™ mass spectrometer. To improve protein identification, we employed three different tryptic peptide fragmentation modes, which included CID, HCD, and ETD to discover proteins involved in the silk assembly pathway and silk fiber. In addition to MaSp1 and MaSp2, we confirmed the presence of a third spidroin AcSp1 in dragline silk, a spidroin widely recognized as the major constituent of wrapping silk. Our findings also reveal that MA glands, spinning dope, and dragline silk contain at least 7 common proteins: major ampullate spidroin 1 and 2 (MaSp1 and MaSp2), 3 members of the Cysteine-Rich Protein Family (CRP1, CRP2 and CRP4), and two uncharacterized proteins, CRISP3 and fasciclin. In summary, this study provides a proteomic blueprint to construct synthetic silk fibers that most closely mimic natural fibers

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Books on the topic "Comprehensive proteomics"

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Marko-Varga, Gyorgy. Proteomics & Peptidomics, Volume 46: New Technology Platforms Elucidating Biology (Comprehensive Analytical Chemistry). Elsevier Science, 2005.

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Bischoff, Rainer, Bruno Domon, Scott Napper, and Berend Hoekman. Comprehensive Biomarker Discovery and Validation for Clinical Application. Royal Society of Chemistry, The, 2013.

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Vermeulen, Roel, Douglas A. Bell, Dean P. Jones, Montserrat Garcia-Closas, Avrum Spira, Teresa W. Wang, Martyn T. Smith, Qing Lan, and Nathaniel Rothman. Application of Biomarkers in Cancer Epidemiology. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0006.

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Advancements in OMICs are now enabling investigators to explore comprehensively the biological consequences of exogenous and endogenous exposures by detecting molecular signatures of exposure, early signs of adverse biological effects, preclinical disease, and molecularly defined cancer subtypes. These new technologies have proven invaluable for assembling a comprehensive portrait of human exposure, health, and disease. This includes hypothesis-driven biomarkers, as well as platforms that can agnostically analyze entire biologic processes and “compartments,” including the measurement of small molecules (metabolomics), DNA polymorphisms and rarer inherited variants (genomics), methylation and microRNA (epigenomics), chromosome-wide alterations, mRNA (transcriptomics), proteins (proteomics), and the microbiome (microbiomics). Although the implementation of these technologies in epidemiologic studies has already shown great promise, some challenges of particular importance must be addressed. Non-genetic OMIC markers vary over time due to both random variation and physiologic changes. Therefore, there is an urgent need for cohorts to collect repeat biological samples over time.

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Raychaudhuri, Soumya. Computational Text Analysis. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198567400.001.0001.

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This book brings together the two disparate worlds of computational text analysis and biology and presents some of the latest methods and applications to proteomics, sequence analysis and gene expression data. Modern genomics generates large and comprehensive data sets but their interpretation requires an understanding of a vast number of genes, their complex functions, and interactions. Keeping up with the literature on a single gene is a challenge itself-for thousands of genes it is simply impossible. Here, Soumya Raychaudhuri presents the techniques and algorithms needed to access and utilize the vast scientific text, i.e. methods that automatically "read" the literature on all the genes. Including background chapters on the necessary biology, statistics and genomics, in addition to practical examples of interpreting many different types of modern experiments, this book is ideal for students and researchers in computational biology, bioinformatics, genomics, statistics and computer science.

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Book chapters on the topic "Comprehensive proteomics"

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de Godoy, Lyris M. F. "SILAC Yeast: From Labeling to Comprehensive Proteome Quantification." In Shotgun Proteomics, 81–109. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0685-7_6.

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Patwa, Tasneem H., Jia Zhao, David E. Misek, and David M. Lubman. "Two-Dimensional Liquid Separations, Protein Microarrays, and Mass Spectrometry in Comprehensive Analysis of Posttranslational Modifications and Biomarker Discovery in Cancers." In Clinical Proteomics, 145–64. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2008. http://dx.doi.org/10.1002/9783527622153.ch11.

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Zhang, Lina, Giacomo Lanzoni, Matteo Battarra, Luca Inverardi, and Qibin Zhang. "Label-Free LC-MS/MS Strategy for Comprehensive Proteomic Profiling of Human Islets Collected Using Laser Capture Microdissection from Frozen Pancreata." In Functional Proteomics, 253–64. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8814-3_16.

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Patel, Jayvadan, and Anita Patel. "Proteomics as a Comprehensive Molecular Means to Understand Dietary Health Effects." In Nutrigenomics and Nutraceuticals, 135–58. Boca Raton : CRC Press, 2017.: CRC Press, 2017. http://dx.doi.org/10.1201/9781315153711-6.

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Edwards, Amanda, and Wilhelm Haas. "Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines." In Methods in Molecular Biology, 1–13. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-3341-9_1.

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Holtz, Anja, Nathan Basisty, and Birgit Schilling. "Quantification and Identification of Post-Translational Modifications Using Modern Proteomics." In Methods in Molecular Biology, 225–35. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_16.

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AbstractPost-translational modifications (PTMs) occur dynamically, allowing cells to quickly respond to changes in the environment. Lysine residues can be targeted by several modifications including acylations (acetylation, succinylation, malonylation, glutarylation, and others), methylation, ubiquitination, and other modifications. One of the most efficient methods for the identification of post-translational modifications is utilizing immunoaffinity enrichment followed by high-resolution mass spectrometry. This workflow can be coupled with comprehensive data-independent acquisition (DIA) mass spectrometry to be a high-throughput, label-free PTM quantification approach. Below we describe a detailed protocol to process tissue by homogenization and proteolytically digest proteins, followed by immunoaffinity enrichment of lysine-acetylated peptides to identify and quantify relative changes of acetylation comparing different conditions.

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Schober, Florian A., Ilian Atanassov, Christoph Freyer, and Anna Wredenberg. "Quantitative Proteomics in Drosophila with Holidic Stable-Isotope Labeling of Amino Acids in Fruit Flies (SILAF)." In Methods in Molecular Biology, 75–87. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0834-0_7.

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AbstractProtein-focused research has been challenging in Drosophila melanogaster due to few specific antibodies for Western blotting and the lack of effective labeling methods for quantitative proteomics. Herein, we describe the preparation of a holidic medium that allows stable-isotope labeling of amino acids in fruit flies (SILAF). Furthermore, in this chapter, we provide a protocol for mitochondrial enrichments from Drosophila larvae and flies together with a procedure to generate high-quality peptides for further analysis by mass spectrometry. Samples obtained following this protocol can be used for various functional studies such as comprehensive proteome profiling or quantitative analysis of posttranslational modifications upon enrichment. SILAF is based on standard fly routines in a basic wet lab environment and provides a flexible and cost-effective tool for quantitative protein expression analysis.

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Hecker, Michael, and Susanne Engelmann. "Physiological Proteomics of Bacillus subtilis and Staphylococcus aureus: Towards a Comprehensive Understanding of Cell Physiology and Pathogenicity." In Pathogenomics, 43–68. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2006. http://dx.doi.org/10.1002/352760801x.ch3.

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Kommu, Sashi S., and Emanuel Petricoin. "The Proteomic Approach to Prostate Cancer." In Prostate Cancer: A Comprehensive Perspective, 157–67. London: Springer London, 2012. http://dx.doi.org/10.1007/978-1-4471-2864-9_13.

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Cassoli, Juliana S., and Daniel Martins-de-Souza. "Comprehensive Shotgun Proteomic Analyses of Oligodendrocytes Using Ion Mobility and Data-Independent Acquisition." In Neuromethods, 65–74. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7119-0_5.

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Conference papers on the topic "Comprehensive proteomics"

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Emaminejad, S., M. T. Barako, R. W. Davis, R. W. Dutton, K. E. Goodson, and M. Javanmard. "MULTIPLEXED PROTEOMICS USING TWO ORDERS OF MAGNITUDE ENHANCED DIELECTROPHORESIS: A COMPREHENSIVE ELECTRICAL AND ELECTROTHERMAL DESIGN METHODOLOGY." In 2014 Solid-State, Actuators, and Microsystems Workshop. San Diego: Transducer Research Foundation, 2014. http://dx.doi.org/10.31438/trf.hh2014.6.

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Tachikawa, Masanori, Daichi Sano, Shota Sasaki, Makoto Kanzaki, Tetsuya Terasaki, and Toshiro Kaneko. "Atmospheric-pressure plasma-induced cellular responses in human colorectal adenocarcinoma Caco-2 cells: A study of comprehensive quantitative proteomics." In 2016 IEEE International Conference on Plasma Science (ICOPS). IEEE, 2016. http://dx.doi.org/10.1109/plasma.2016.7534130.

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Benz, Stephen, J. Zackary Sanborn, Nicole S. Hensley, Todd Hembrough, Charles J. Vaske, Jon Burrows, Shahrooz Rabizadeh, Ivor Royston, and Patrick Soon-Shiong. "Abstract 25: Whole genome sequencing and quantitative proteomics reveal HPV integration and HER2 overexpression in a patient with cervical cancer: Comprehensive omics analysis driving clinical treatment decisions." In Abstracts: AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; June 13-16, 2015; Salt Lake City, UT. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1557-3265.pmsclingen15-25.

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Mukherjee, Seema, Yoshitsugu Mitani, Robert Cardnell, You Hong Fan, Lixia Diao, Jing Wang, Adel K. El-Naggar, and Lauren Averette Byers. "Abstract LB-111: Comprehensive proteomic analysis of salivary gland cancer subtypes." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-lb-111.

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Teng, Pang-ning, Brian L. Hood, Tracy Litzi, Nicole P. Chappell, Chad A. Hamilton, G. Larry Maxwell, and Thomas P. Conrads. "Abstract 799: Comprehensive proteomic analysis of cisplatin resistance in ovarian cancer." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-799.

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Rodland, Karin D. "Abstract IA10: Comprehensive proteomic analyses of TCGA ovarian cancer specimens: Update from CPTAC." In Abstracts: AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; September 18-21, 2013; Miami, FL. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1078-0432.ovca13-ia10.

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Pacharawongsakda, Eakasit, Sunai Yokwai, Nitsara Karoonuthaisiri, Duangdao Wichadakul, and Supawadee Ingsriswang. "ESTplus: An Integrative System for Comprehensive and Customized EST Analysis and Proteomic Data Matching." In 2008 2nd International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2008. http://dx.doi.org/10.1109/icbbe.2008.14.

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Hosseini-Beheshti, Elham, Steven Pham, Hans Adomat, and Emma S. (Tomlinson) Guns. "Abstract 440: Characterization and comprehensive proteomic analysis of exosomes derived from prostate cancer cell lines." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-440.

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Mammen, Manoj J., Jun Qu, and Sanjay Sethi. "Comprehensive Proteomic Profiling Of Bronchoalveolar Lavage Fluid Of Individuals With COPD Compared To Healthy Controls." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3747.

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Fedorenko, Inna V., Kim H. T. Paraiso, Bin Fang, John M. Koomen, and Keiran S. M. Smalley. "Abstract IA04: Using comprehensive proteomic approaches to map signaling adaptations to BRAF and BRAF/MEK inhibition." In Abstracts: AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; June 18-21, 2014; Orlando, FL. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1557-3265.pms14-ia04.

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