SHIRLEY, Oct 30th, 2017 - Creative Proteomics, a world leading proteomics identification and analysis service provider. Except for the professional services, we also collect the newest biostatistics and bioinformatics tools that can be used to interpret proteomics data.. Proteomics experiments often produce large amounts of data. However, the simple identification and quantification of proteins from cell proteome or subtype proteins is not sufficient to adequately understand the complex mechanisms that occur in biological systems. Thus, the functional annotation analysis of the protein data set using the bioinformatics tool is critical to explaining the results of high-throughput proteomics. Although large-scale proteomics data are rapidly increasing, the biological interpretation of these results remains a challenging task. Biostatistics and bioinformatics tools have started to be applied in the interpretation of the proteomics data:. .GO functional annotation for proteomics data.. Functional ...
TY - JOUR. T1 - Mining gene functional networks to improve mass-spectrometry-based protein identification. AU - Ramakrishnan, Smriti R.. AU - Vogel, Christine. AU - Kwon, Taejoon. AU - Penalva, Luiz O. AU - Marcotte, Edward M.. AU - Miranker, Daniel P.. PY - 2009/11/15. Y1 - 2009/11/15. N2 - Motivation: High-throughput protein identification experiments based on tandem mass spectrometry (MS/MS) often suffer from low sensitivity and low-confidence protein identifications. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other evidence to suggest that a protein is present and confidence in individual protein identification can be updated accordingly. Results: We develop a method that analyzes MS/MS experiments in the larger context of the biological processes active in a cell. Our method, MSNet, improves protein identification in shotgun proteomics experiments by considering information on functional associations ...
IKKbeta is the key kinase in the TNFalpha-NF-kB pathway that phosphorylates IkBalpha and targets it for polyubiquitination and degradation. As a result, NF-kB is released and moves into the nucleus, where it binds to the promoters of target genes and activates transcription that increases cell proliferation or prevents apoptosis. In the chapter two of this dissertation, a novel role for the TNFalpha-IKK-NF-kB signaling pathway in anti-cancer drug resistance is described. Contrary to its physiological function, TNFalpha induced G0-G1 cell cycle arrest through IKK in cancer cells, which provided a mechanism for developing drug resistance to the purine and pyrimidine antimetabolites. A specific IKKbeta inhibitor prevented TNFalpha-induced drug resistance. Thus IKK inhibitors can enhance the effectiveness of antimetabolites in chemotherapy.; Phosphorylation regulates the kinase activity of IKKbeta. In chapters three and four of this dissertation, mass spectrometry-based proteomic methods was ...
TY - JOUR. T1 - Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions. AU - de Jong, Ebbing P.. AU - Xie, Hongwei. AU - Onsongo, Getiria. AU - Stone, Matthew D.. AU - Chen, Xiao Bing. AU - Kooren, Joel A.. AU - Refsland, Eric W.. AU - Griffin, Robert J.. AU - Ondrey, Frank G.. AU - Wu, Baolin. AU - Le, Chap T.. AU - Rhodus, Nelson L.. AU - Carlis, John V.. AU - Griffin, Timothy J.. PY - 2010/8/11. Y1 - 2010/8/11. N2 - Background Oral cancer survival rates increase significantly when it is detected and treated early. Unfortunately, clinicians now lack tests which easily and reliably distinguish pre-malignant oral lesions from those already transitioned to malignancy. A test for proteins, ones found in non-invasively-collected whole saliva and whose abundances distinguish these lesion types, would meet this critical need. Methodology/Principal Findings To discover such proteins, in a first-of-its-kind study we ...
TY - JOUR. T1 - Quantitative proteomics analysis of human endothelial cell membrane rafts. T2 - Evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induce barrier enhancement. AU - Guo, Yurong. AU - Singleton, Patrick A.. AU - Rowshan, Austin. AU - Gucek, Marjan. AU - Cole, Robert N.. AU - Graham, David R.M.. AU - Van Eyk, Jennifer E.. AU - Garcia, Joe G.N.. PY - 2007/4/1. Y1 - 2007/4/1. N2 - Endothelial cell barrier dysfunction results in the increased vascular permeability observed in inflammation, tumor metastasis, angiogenesis, and atherosclerosis. Sphingosine 1-phosphate (S1P), a biologically active phosphorylated lipid growth factor released from activated platelets, enhances the endothelial cell barrier integrity in vitro and in vivo. To begin to identify the molecular mechanisms mediating S1P induced endothelial barrier enhancement, quantitative proteomics analysis (iTRAO™) was performed on membrane rafts isolated from human pulmonary artery endothelial cells in the ...
In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics.
In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics.
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.. Protein phosphorylation events during T cell receptor (TCR) signaling control the formation of complexes among proteins proximal to the TCR, the activation of kinase cascades, and the activation of transcription factors; however, the mode and extent of the influence of phosphorylation in coordinating the diverse phenomena associated with T cell activation are unclear. Therefore, we used the human Jurkat T cell leukemia cell line as a model system and performed large-scale quantitative phosphoproteomic analyses of TCR signaling. We identified 10,665 unique phosphorylation sites, of which 696 showed TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation data sets to uncover underlying mechanisms associated with T cell activation. We found that, upon stimulation of the TCR, phosphorylation events extensively targeted protein modules involved in all of the salient phenomena associated ...
Liquid chromatography-mass spectrometry (LC-MS)-based proteomics studies of large sample cohorts can easily require from months to years to complete. Acquiring consistent, high-quality data in such large-scale studies is challenging because of normal variations in instrumentation performance over time, as well as artifacts introduced by the samples themselves, such as those due to collection, storage and processing. Existing quality control methods for proteomics data primarily focus on post-hoc analysis to remove low-quality data that would degrade downstream statistics; they are not designed to evaluate the data in near real-time, which would allow for interventions as soon as deviations in data quality are detected. In addition to flagging analyses that demonstrate outlier behavior, evaluating how the data structure changes over time can aide in understanding typical instrument performance or identify issues such as a degradation in data quality due to the need for instrument cleaning and/or ...
Creative Proteomics is the proteomics division of CD Inc, an integrated CRO company that provides a full range of drug development services, including Molecular Biology, Biochemistry, Systems Biology, Organic Chemistry, Genomics, Bioinformatics, Structural Biology, Preclinical and Clinical studies. Creative Proteomics specializes in a full range of services to support various proteome-related researches from identification of single proteins to large-scale proteomic studies. We have one of the most advanced proteomics platforms in the world and our staff scientists are experienced proteomics professionals. Our proteome analysis platform provides protein separation, characterization, identification and quantification services, featured with high throughput and super-sensitivity. In addition, analyses of protein post-translational modifications such as phosphorylation and glycosylation are available. Creative Proteomics is staffed by specialists who are extensively experienced in handling hard-to
TY - JOUR. T1 - An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation. AU - Kalesh, Karunakaran. AU - Lukauskas, Saulius. AU - Borg, Aaron J.. AU - Snijders, Ambrosius P.. AU - Ayyappan, Vinay. AU - Leung, Anthony K.L.. AU - Haskard, Dorian O.. AU - DiMaggio, Peter A.. PY - 2019/12/1. Y1 - 2019/12/1. N2 - ADP-ribosylation is integral to a diverse range of cellular processes such as DNA repair, chromatin regulation and RNA processing. However, proteome-wide investigation of its cellular functions has been limited due to numerous technical challenges including the complexity of the poly(ADP-ribose) (PAR) chains, low abundance of the modification and lack of sensitive enrichment methods. We herein show that an adenosine analogue with a terminal alkyne functionality at position 2 of the adenine (2-alkyne adenosine or 2YnAd) is suitable for selective enrichment, fluorescence detection and mass spectrometry proteomics analysis of the candidate ...
Proteomics Industry Overview. Global Proteomics Market was valued at $17,988 million in 2015, and is expected to reach $44,452 million by 2022, supported by a CAGR of 13.7%. Proteomics is the study of the structure and functions of proteins that can be used in the drug discovery, diagnosis, and treatment of diseases. A proteome is never constant as it differs from one cell to other with time. Proteomics is used to evaluate the rate of protein production, interaction of proteins with one another, involvement of proteins in metabolic pathways, and modification of proteins. In addition, it finds extensive applications in drug discovery, development of personalized medicines, and identification of markers for disease diagnosis, which has led to the stellar growth of the proteomics market in the past few years. With the increase in awareness regarding the benefits of personalized medicines, companies and government organizations have increased their R&D expenditure on the development of proteomics. ...
Lung cancer is the most common cause of cancer-related death worldwide, less than 7% of patients survive 10 years following diagnosis across all stages of lung cancer. Late stage of diagnosis and lack of effective and personalized medicine reflect the need for a better understanding of the mechanisms that underlie lung cancer progression. Quantitative proteomics provides the relative different protein abundance in normal and cancer patients which offers the information for molecular interactions, signaling pathways, and biomarker identification. Here we introduce both theoretical and practical applications in the use of quantitative proteomics approaches, with principles of current technologies and methodologies including gel-based, label free, stable isotope labeling as well as targeted proteomics. Predictive markers of drug resistance, candidate biomarkers for diagnosis, and prognostic markers in lung cancer have also been discovered and analyzed by quantitative proteomic analysis. Moreover,
Additional file 9: of Comparative proteomic analysis reveals a dynamic pollen plasma membrane protein map and the membrane landscape of receptor-like kinases and transporters important for pollen tube growth and interaction with pistils in rice
Background and Description: As in all shotgun proteomics experiments, global quantitative phosphoproteomics relies heavily on appropriate bioinformatics analyses. The relevant bioinformatics methods associated with global quantitative phosphoproteomics are confident identification and validation of thousands of phosphopeptides from MS/MS spectra, determination of phosphorylation stoichiometry of phosphopeptides, localization of phosphorylation sites, and measurement of the ratio of phosphorylated peptides. Each one of these steps is of equal importance. That is, if any one of these steps is inaccurate or of low confidence, the entire quantitative analysis is equally inaccurate and of low confidence. Identification of phosphopeptide sequences and measurement of phosphorylated peptides leverages the accuracy of global quantitative proteomics (i.e. SEQUEST, ProLuCID, DTASelect, and CENSUS). When the appropriate filtering methods are used, these two steps are already of high confidence. The ...
Yie, H.L., Boelsterli, U.A., Lin, Q., Chung, M.C.M. (2008). Proteomics profiling of hepatic mitochondria in heterozygous Sod2+/-mice, an animal model of discreet mitochondrial oxidative stress. Proteomics 8 (3) : 555-568. [email protected] Repository. https://doi.org/10.1002/pmic. ...
The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease
A bottom-up label-free mass spectrometric proteomic strategy was used to analyse the protein profiles of the human embryonic secretome. Culture media samples used for embryonic culture of patients undergoing intracytoplasmic sperm injection cycles were selected as a test case for this exploratory proof-of-principle study. The media were stored after embryo transfer and then pooled into positive (n = 8) and negative (n = 8) implantation groups. The absolute quantitative bottom-up technique employed a multidimensional protein identification technology based on separation by nano-ultra-high pressure chromatography and identification via tandem nano-electrospray ionization mass spectrometry with data-independent scanning in a hydrid QqTOF mass spectrometer. By applying quantitative bottom-up proteomics, unique proteins were found exclusively in both the positive- and negative-implantation groups, which suggest that competent embryos express and secrete unique biomarker proteins into the surrounding ...
phdthesis{be258743-7e2f-4e1a-b45d-bbfdaaa3d645, abstract = {Proteomics is expected to generate new insights into biological processes as well as identify novel biomarkers and therapeutic targets since most biological functions are transmitted through proteins. However, due to the complexity displayed by a proteome and inherent limitations associated with current methodologies, proteomic analyses often result in incomplete coverage and inconsistent measurements. Clearly, the development of novel high-performing proteomic platforms will be essential in order to successfully decipher the human proteome(s).,br/,,br, ,br/,,br, This thesis, based on four original papers denoted I to IV, describes the development and applicability of a novel proteomic technology platform entitled Global Proteome Survey (GPS) capable of transforming affinity proteomics into a global discovery engine. The GPS methodology combines the best features of affinity proteomics and mass spectrometry, and is based on using ...
TY - JOUR. T1 - Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. AU - Matthiesen, Rune. AU - Carvalho, Ana Sofia. PY - 2020/1/1. Y1 - 2020/1/1. N2 - Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their ...
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TY - JOUR. T1 - Cross-species analysis of nicotine-induced proteomic alterations in pancreatic cells. AU - Paulo, Joao A.. AU - Urrutia, Raul. AU - Kadiyala, Vivek. AU - Banks, Peter. AU - Conwell, Darwin L.. AU - Steen, Hanno. PY - 2013/5. Y1 - 2013/5. N2 - Toxic compounds in tobacco, such as nicotine, may adversely affect pancreatic function. We aim to determine nicotine-induced protein alterations in pancreatic cells, thereby revealing links between nicotine exposure and pancreatic disease. We compared the proteomic alterations induced by nicotine treatment in cultured pancreatic cells (mouse, rat, and human stellate cells and human duct cells) using MS-based techniques, specifically SDS-PAGE (gel) coupled with LC-MS/MS and spectral counting. We identified thousands of proteins in pancreatic cells, hundreds of which were identified exclusively or in higher abundance in either nicotine-treated or untreated cells. Interspecies comparisons of stellate cell proteins revealed several ...
Purpose: Polymorphisms in tissue inhibitor of metalloproteinase 3 (TIMP3) have been associated with Sorsby fundus dystrophy (SFD) and age-related macular degeneration. Toward a molecular understanding of TIMP3 dysfunction, we pursued quantitative proteomic analyses of the retina and choroid from TIMP-3 knockout (KO) mice and knockin (KI) mice expressing the TIMP3 S156C mutation that causes SFD.. Methods: Soluble proteins from isolated retinas and choroid-containing posterior globes from TIMP3 KO mice (n = 5 mice), KI homozygotes (n = 5), KI heterozygotes (n = 4), and wild-type mice (n = 7) were quantified by iTRAQ technology. Protein was digested with trypsin, peptides labeled with iTRAQ tags, fractionated by strong cation exchange chromatography, and peptides were analyzed by LC MS/MS. Proteins were identified using the Swiss-Protein database and quantified using code written in R. Proteins quantified with ≥ 2 unique peptides/protein in ≥ 3 mice/strain were considered significantly altered ...
The recent explosion in available genomic and protein sequence information is providing a sequence infrastructure for the emerging field of proteomics. A major aspect of many proteomics strategies is the identification of proteins using an analytical "fingerprint" that can be used to search a sequence database. One common "fingerprint" is the tandem mass (MS/MS) spectrum of a peptide. Thus, an MS/MS spectrum can be algorithmically compared with predicted peptide spectra from a sequence database to identify the respective protein (1, 2). The digestion of intact protein mixtures followed by the direct analysis of the resulting peptides by capillary liquid chromatography-MS/MS has facilitated "shotgun" identification of protein mixtures without the need for prior sample fractionation (3). Combined with the recent development of capillary multidimensional liquid chromatography [multidimensional protein identification technology (MudPIT)], this approach is now capable of characterizing proteins ...
This session provides an introduction to Mass spectrometry Proteomics at the European Bioinformatics Institute (EBI). Further information for this session is available. This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see Related Courses section below). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.. ...
Proteomics is concerned with the large-scale study of proteins. Beyond structural and functional analysis of individual proteins, proteomics research seeks to
IMPORTANCE OF IRON IN PLANTIron (Fe) is an essential micronutrient and its deficiency is a serious nutritional problem for all living organisms. This is because Fe is not only a basic requirement in cellular functions such as the redox reactions in photosynthesis and respiration, but is also required in the enzymatic processes like DNA replication, lipid metabolism, and nitrogen fixation in plants (Lan et al., 2011; Briat et al., 2015). As the photosynthetic apparatus contains much Fe, involved in many metabolic reactions in plastids, it becomes an important factor for survival of green plants. In plants, Fe deficiency can be observed by the development of chlorosis, which reduces the photosynthetic activity (Spiller et al., 1980; Terry, 1980; Straus, 1994; Briat et al., 2015). PROTEOMICS STUDIES RELATED TO IRON DEFICIENCY Proteomics is being increasingly used to expand our understanding of plant growth and development under both normal and stressful environmental conditions (Agrawal and Rakwal, 2008).
Quantitation is an inherent requirement in comparative proteomics and there is no exception to this for plant proteomics. Quantitative proteomics has high demands on the experimental workflow, requiring a thorough design and often a complex multi-step structure. It has to include sufficient numbers of biological and technical replicates and methods that are able to facilitate a quantitative signal read-out. Quantitative plant proteomics in particular poses many additional challenges but because of the nature of plants it also offers some potential advantages. In general, analysis of plants has been less prominent in proteomics. Low protein concentration, difficulties in protein extraction, genome multiploidy, high Rubisco abundance in green tissue, and an absence of well-annotated and completed genome sequences are some of the main challenges in plant proteomics. However, the latter is now changing with several genomes emerging for model plants and crops such as potato, tomato, soybean, rice, maize and
The Proteomics Identification Database (PRIDE) was established in 2005 in response to the large amounts of proteomic data. This is not the only database that serves as a repository of proteomics data. Others include GPMDB, Proteinpedia, Peptide Atlas, and NCBIs Peptidome. The data submitted to the PRIDE database can be anonymously shared with reviewers and editors through log-in accounts. This feature has made the PRIDE database the preferred placed to submit data for a variety of journals including Nature Biotechnology, Proteomics, and Nature Methods. There have been two tools that have had a very positive influence on the growth of the PRIDE database. These are the Ontology Lookup Service (OLS) and the Protein Identifier Cross-Reference System (PICR). Database on Demand (DoD) is a third tool that was added to increase the usefulness of the database.. The data contained within PRIDE is very diverse and is becoming more diverse as the years pass by. As of 2010, humans are represented the most ...
In their Perspective, Schubert et al. discuss developments and challenges in mass-spectrometry-based proteomics technology in the past decade and explore its role in molecular systems biology, clinical research and personalized medicine. In this Perspective, we discuss developments in mass-spectrometry-based proteomic technology over the past decade from the viewpoint of our laboratory. We also reflect on existing challenges and limitations, and explore the current and future roles of quantitative proteomics in molecular systems biology, clinical research and personalized medicine.
Eukaryotic cells segregate and organize functionally related proteins into discrete compartments that have distinct structures and functions. Previous organelle proteomics studies have mainly focused on one compartment, providing insights into the biology and functions of these structures. Recently two groups performed magnificent proteomics studies on multiple organelles in mouse organ by combining subcellular fractionation and mass spectrometry technologies (8, 19). However, no comprehensive characterization of a single human cell type has been carried out to date. In this study, we combined replicate proteomics analyses and extensive subcellular fractionation/enrichment methods in Jurkat cells, identifying 5381 proteins of which 80% were assigned with at least one unambiguous peptide sequence. Based on comparison between proteomics and transcriptomics profiling in Jurkat cells, we were able to specifically exclude redundant entries and potential false positive identifications, resulting in ...
Current Proteomics research in the emerging field of proteomics is growing at an extremely rapid rate. The principal aim of Current Proteomics is to publish well-timed review articles in this fast-expanding area on topics relevant and significant to the development of proteomics. Current Proteomics is an essential journal for everyone involved in proteomics and related fields in both academia and industry.. ...
Contents for Genetics. VOLUME 1.. Contents for Genomics.. Contents for Proteomics.. Contents for Bioinformatics.. List of Contributors to Genetics.. Preface.. 1. Genetic Variation and Evolution.. 2. Cytogenetics.. 3. Epigenetics.. 4. Gene Mapping.. VOLUME 2.. 5. Comlex Triats and Deseases.. 6. Genetic Medicine and Clinical Genetics.. 7. Gene Theory.. Contents for Genomics.. VOLUME 3.. 1. Genome Sequencing.. 2. Mapping.. 3. The Human Genome.. 4. Model Organisms: Functional and Comparative Genomics.. VOLUME 4.. 1. Bacteria and Other Pathogens.. 2. SNPs/Haplotypes.. 3. ESTs: Cancer Genes and the Anatomy Project.. 4. Expression Profiling.. Contents for Proteomics.. VOLUME 5.. 1. Core Methodologies.. 2. Expression Protemics.. 3. Mapping of Biochemical Networks.. 4. Functional Proteomics.. VOLUME 6.. 5. Proteome Diversity.. 6. Proteome Families.. 7. Structural Proteomics.. 8. System Biology.. Contents for Bioinformatics.. VOLUME 7.. 1. Genome Assembly and Sequencing.. 2. Gene Finding and Gene ...
One of the constant challenges for proteomics is inadequate protein identification because of the interference of high abundance proteins (1). The challenge is particularly critical for plant proteomics analysis because of the prevalence of Rubisco (Ribulose-1,5-bisphosphate carboxylase oxygenase) in green tissue. As a major enzyme involved in carbon fixation, Rubisco consists of 30 to 50% of total plant protein from green tissues and causes less sensitivity, dynamic range, and protein identification of plant proteomics (2⇓-4). Influences of high abundance proteins like Rubisco affect both gel-based and shot-gun proteomics analysis. In one of the most popular shot-gun proteomics platforms with the data-dependent MS/MS acquisition, the peptides derived from the abundant proteins have more chance to be sampled by the MS instrument than the peptides from other functional proteins. Thus, the dynamic range and detection sensitivity will be sacrificed because of the prevalence of high abundance ...
Hagenstein, M., Kruse, O., & Sewald, N. (2008). Chemical Proteomics. In G. K. Agrawal & R. Rakwal (Eds.), Plant Proteomics: Technologies, Strategies and Applications (pp. 47-59). Hoboken: J. Wiley & Sons. doi:10.1002/9780470369630. ...
Enhanced qualitative and quantitative proteomic analysis using pSMART combines data dependent and data independent acquisition for improved results.
AB SCIEX today introduced the TripleTOF® 6600 system with SWATH™ Acquisition 2.0 - the companys revolutionary solution for quantitative proteomics.
Proteomic profiling and mass spectrometry - posted in Protein and Proteomics: Hello All! Two-dimensional polyacrylamide gel electrophoresis remains a very popular option for global proteomic profiling for its accessibility and low cost. 2-DE has notable drawbacks relative to shotgun proteomics (insufficient resolving power results in multiple proteins per spot, not well-suited to membrane proteins, follow-up by tandem protein mass spectrometry required to ID proteins, etc.). However, t...
In this study, we used quantitative proteomics to identify a panel of proteins whose change in abundance upon treatment correlates with sensitivity to EGFR tyrosine kinase inhibition across a number of cell lines and in an in vivo (isogenic sensitive/resistant) xenograft model. We also showed differences between baseline abundance and levels of certain proteins after gefitinib treatment in gefitinib-sensitive versus -resistant NSCLC cell lines (Table 1, Supplementary Fig. S4). Several proteins showed changes dependent on gefitinib treatment in an in vivo tumor model (Fig. 3). The results presented highlight a proteomics paradigm, where discovery in vitro successfully translates to concordant behavior in vivo. In addition, our model-based, but broad-scale, approach allowed for significant and diverse investigation of the specificity and generality of discovered proteins. An alternate panel discovery strategy may have been to investigate the known members of the EGFR signaling axis. However, as ...
Proteome is a complement of proteins expressed in a cell at given time and proteomics means global analysis of this protein complement. Proteomics investigates the global changes of proteins in cells and tissues in response to a stimulus (for example temperature change, drug or nutrient treatment, or growth phase). It also studies protein-protein interactions. Proteomics came into prominence after 1997 and quickly became a popular research avenue, holding much greater importance than scientists initially suspected. The main reason for this is the fact that based on the genomic sequence it is impossible to predict how the gene products (proteins) are going to behave. Proteins are regulated at the level of protein translation, subsequently they can be modified by addition of various molecules (sugar, for example). Proteins can have varying half-lives, and their intracellular distribution can be predicted only with limited certainty.. ...
Buy, download and read Redox Proteomics ebook online in PDF format for iPhone, iPad, Android, Computer and Mobile readers. Author: Isabella Dalle-Donne; Andrea Scaloni; D. Allan Butterfield; Dominic M. Desiderio; Nico M. Nibbering. ISBN: 9780471973119. Publisher: Wiley. Methodology and applications of redox proteomics The relatively new and rapidly changing field of redox proteomics has the potential to revolutionize how we diagnose disease, assess risks, determin
Background: Selection of patients to receive a primary prevention ICD is solely based on LV EF. Plasma biomarkers may compliment this but most have not been evaluated in predicting arrhythmic death. We determined whether plasma proteomic profiling could afford an unbiased, discovery based approach to identify novel biomarkers to predict cause specific event rates from SCA (arrhythmic death or defibrillation for VT/VF).. Methods: Plasma samples were obtained at entry in 203 patients in the PAREPET study. Proteomic profiling was performed in a subset of 10 patients with SCA vs. 10 survivors matched for EF (26%), age (66 years) and creatinine (1.4). We used a tandem affinity depletion method (IgY14-SuperMix) to reduce high- and medium- abundance plasma proteins, followed by extensive ion current based biomarker discovery. Plasma proteins were expressed as SCA/survivors.. Results: SCA developed 1016±735 days after sampling. Stringent cutoff criteria (0.3% peptide identification FDR ; ≥2 unique ...
International Journal of Proteomics is a peer-reviewed, Open Access journal that publishes original research articles as well as review articles in all areas of proteomics.
Epigenetic reprogramming is thought to play an important role during monocyte differentiation. Complementary to cell surface markers, the characterization of monocytic cell lineages by mass spectrometry based protein/histone expression profiling opens a new avenue for studying immune cell differentiation. Here, we report the application of mass spectrometry and bioinformatics to identify changes in human monocytes during their differentiation into macrophages and dendritic cells. Our data show that linker histone H1 proteins are significantly down-regulated during monocyte differentiation. While highly enriched H3K9-methyl/S10-phos/K14-acetyl tri-modification forms of histone H3 were identified in monocytes and macrophages, they were dramatically reduced in dendritic cells. In contrast, histone H4 K16 acetylation was found to be markedly higher in dendritic cells than in monocytes and macrophages. We also found that global hyperacetylation generated by the nonspecific histone deacetylase HDAC ...
The intersection of bioinformatics and proteomics allows for the generation and management of large amounts of data. High-throughput computational methods are an integral part of proteomics for data acquisition, storage, and analysis. The Internet allows easy sharing of data sets and information between researchers and laymen. Large public and private databases are now common, and scientists of all expertise levels from all over the world can contribute to them. The Protein Data Bank (PDB) is one such database, handling structure and sequence data for proteins with a determined crystal structure. One of the largest databases, by far, is the National Center for Biotechnology Information, or NCBI. It contains both curated literature and links to many databases and resources for proteomics and biology in general.. Predictions and data gained from these "in-silico" methods cannot always be used in place of laboratory data. Whether or not they can be used depends on the data type and the situation ...
Plasma proteomics reveals gestational age-specific responses to mechanical ventilation and identifies the mechanistic pathways that initiate preterm lung injury
The PASEF capability represents a step-change improvement in performance as it delivers higher-sensitivity and higher-speed shotgun proteomics without loss of mass resolution. Higher scan speeds result in lower mass resolution in FT-based MS technology commonly used for shotgun proteomics. These critical limitations are eliminated by PASEF, allowing for a duty cycle near 100% with high sensitivity while maintaining ultra-high mass resolution for both the precursor and the product ions. This key PASEF capability leveraging the dual TIMS technology gives scientists the tools to dig deeper into the complex biology of the cellular machinery and the potential to discover low-level, biologically significant proteins, or validate them in translational and clinical proteomics research on large cohort sizes and in longitudinal studies. Quantitative proteomics is a key area of research in proteomics, and dual TIMS-powered PASEF provides an inherent advantage over the limitations of gated, tandem-in-time, ...
In the previous few years, the PX consortium has established itself as a community-responsive set of dependable proteomics knowledge repositories to allow knowledge submission and dissemination of MS proteomics experiments. With help from funding companies and scientific journals, PX is actively altering the information sharing tradition within the area by selling and enabling sharing of proteomics knowledge within the public area. For instance, after assessing the steadiness of PX assets, since July 2015, the journal Molecular and Cellular Proteomics, one of probably the most outstanding proteomics scientific journals, is now once more mandating deposition of uncooked knowledge with each submitted manuscript , and different journals are transferring on this course (e.g. journals from the Nature and PLOS teams). In this context, public knowledge availability and sharing within the area are shortly turning into the norm, as demonstrated by the excessive knowledge submissions ...
Phosphorylation-driven cell signaling governs most biological functions and is widely studied using mass-spectrometry-based phosphoproteomics. Identifying the peptides and localizing the phosphorylation sites within them from the raw data is challenging and can be performed by several algorithms that return scores that are not directly comparable. This increases the heterogeneity among published phosphoproteomics data sets and prevents their direct integration. Here we compare 22 pipelines implemented in the main software tools used for bottom-up phosphoproteomics analysis (MaxQuant, Proteome Discoverer, PeptideShaker). We test six search engines (Andromeda, Comet, Mascot, MS Amanda, SequestHT, and X!Tandem) in combination with several localization scoring algorithms (delta score, D-score, PTM-score, phosphoRS, and Ascore). We show that these follow very different score distributions, which can lead to different false localization rates for the same threshold. We provide a strategy to ...
Pressure BioSciences is a life sciences company focused on the development and commercialization of a novel, enabling platform technology called Pressure Cycling Technology.
Comparative proteomic approaches for the isolation of proteins interacting with thioredoxin.: Thioredoxin (TRX) is a small multifunctional protein with a disulf
The goal of this workshop is to foster scientific exchange between scientists working on the chromatin proteome, the dynamic behavior of proteins in the nucleus and the integration and visualization of protein and DNA networks. There will be dedicated sessions on the proteomic analysis of histone modifications, of defined chromosomal domains and of functional proteomics together with sessions on quantitative proteomics, emerging technologies and bioinformatic analysis of large proteomic datasets and their visualization, with lectures given by leading researchers in the field. There will also be two poster sessions and several short oral presentations by junior researchers that will be selected from the abstracts.. In addition, major features of the workshop will be the one-on-one "Problem-Solving" sessions where junior researchers can "book" a meeting with one of the expert speakers of the workshop to discuss issues related to their own projects and the «Meet-the-experts-sessions» where three ...
To estimate absolute protein contents in complex mixtures, we previously defined a protein abundance index (PAI) as the number of observed peptides divided by the number of observable peptides per protein (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome. Res. 12, 1231-1245). Here we report that PAI values obtained at different concentrations of serum albumin show a linear relationship with the logarithm of protein concentration in LC-MS/MS experiments. This was also the case for 46 proteins in a mouse whole cell lysate. For absolute quantitation, PAI was converted to exponentially modified PAI (emPAI), equal to 10PAI minus one, which is proportional to protein content in a protein mixture..... ...
Proteomics Company Bioproximity provides full range of proteomic services, including mass spectrometry analysis, protein identification and characterization, protein sequence analysis and so on.
Hagenstein, M. C., Mussgnug, J. H., Lotte, K., Plessow, R., Brockhinke, A., Kruse, O., & Sewald, N. (2003). Affinity-based tagging of protein families with reversible inhibitors: A concept for functional proteomics. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 42(45), 5635-5638. doi:10.1002/anie. ...
Shotgun proteomics is amazing at identifying peptide spectral matches (PSMs). This is what we get out of the instrument: an MS/MS spectra that we can match to something with high confidence to something in our database. The tricky part is getting relevant biological data back out. Figuring out exactly what PSM belongs to what peptide and what peptide belongs to which protein is the hard part. Evolution is working against us here -- it is much easier from a biological standpoint to make proteins with new functions from similar protein than it is to make a new one from scratch ...
Biomonitoring of aquatic environment and assessment of ecosystem health play essential roles in the development of effective strategies for the protection of the environment, human health and sustainable development. Biomarkers of pollution exposure have been extensively utilized in the last few decades to monitor the health of organisms and hence assess environmental status. However, the use of single biomarkers against biotic or abiotic stressors may be limited by the lack of sensitivity and specificity. Therefore, more recently, the search for novel biomarkers has been focused on the application of OMICS methodologies. Environmental proteomics focuses on the analysis of an organisms proteome and the detection of changes in the level of individual proteins/peptides in response to environmental stressors. Proteomics can provide a more robust approach for the assessment of environmental stress and therefore exposure to pollutants. This review aims to summarize the proteomic research in bivalves, ...
To aid in our proteomic studies, we have developed several proteomic tools and methods that facilitate quantitative studies of signaling pathways and protein modifications such as phosphorylation and ubiquitylation. A key system is our proteomics platform called CompPASS (Comparative Proteomics Analysis Software Suite) (Sowa et al., Cell, 2009). CompPASS is designed to help facilitate the identification of high confidence candidate interacting proteins from IP-MS/MS data. The CompPASS website contains all of the data from the Cell paper describing the deubiquitinating enzyme interactome, the autophagy interactome (Nature, 2010), and ERAD interactome (Nature Cell Biology, 2011), as well as tools for navigating this data, and a CompPASS tutorial. This software can be accessed by clicking on the CompPASS icon (below). We have used this approach to examine the interaction partners of hundreds of proteins involved in signal transduction and disease. Recently, we have developed a new method called ...
The lectures cover what Matthias considers the absolute basics in mass spec and proteomics, including the newest methods developed in the last years. The aim would be that this basic knowledge will help you designing better experiments and understand possibilities as well as limitations of proteomics.. PGR students should register attendance in the usual manner (https://workshops.ncl.ac.uk/) so that the session appears in your eportfolio. Post-docs and PIs do not need to register.. Mon Jan 22nd 2018, 15:00 (Mass spec basics 1 - basic of mass measurement, ionisation techniques) Dental Lecture Theatre E. Mon Jan 29th 2018, 15:00 (Mass spec basics 2 - mass analysers, detectors, tandem mass spectrometry) RB Green Lecture Theatre, Dental School. Mon Feb 5th 2018, 15:00 (Mass spec basics 3 - fragmentation techniques, hybrid instruments) Dental Lecture Theatre E. Mon Feb 12th 2018, 15:00 (Proteomics basics 1 - what is proteomics?, sample preparation, experimental design) Dental Lecture Theatre F. Mon ...
Worldwide scientific leaders are gathering from USA, Europe, Middle East,Asia Pacific and Australia at Mass Spectrometry Congress and International Mass Spectrometry and Proteomics Conferences, Events, Meetings planned from May 20-21, 2019 Rome, Italy
SHIRLEY - Sep 30th, 2017 - Creative Proteomics, which specializes in a full range of services to support various proteome-related researches from identification of single proteins to large-scale proteomic studies. Besides, we also offer professional products to support further researches and studies. Such as the Stable Isotope Standard, that will be helpful for the proteomics research use.. Stable isotope labeling with amino acids is the new technology that is used for halo analysis of protein expression by taking advantage of stable isotope labeling amino acid binding mass spectrometry in the cell culture process. It can provide support for qualitative analysis of the protein, also offer accurate quantitative analysis with fewer sample requirements, but the simple and efficient process.. The applications and specific strategies of SILAC technology are in the continuous development of updates. There are many applications and improvements, such as the differential expression of proteins, ...
Proteomics is a systematic study of proteins on a large scale, particularly their functions and structures. Proteomics has the potential to answer some key questions that were unsolved by genomics, because proteins are the functional unit of cells. Proteomics research is enhanced by both protein and DNA sequence databases, advances in mass spectrometry, and development of computer algorithms for database searching. The most common application of proteomics is the analysis of target proteins. Proteomics requires various instruments, consumables, reagents, media, and software for protein identification, purification, quantification, and investigation of the interaction between various proteins. Proteins can undergo post-translational modifications to form three-dimensional structures, which can easily be identified by proteomics.. TechNavios analysts forecast the Global Proteomics market to grow at a CAGR of 8.39 percent over the period 2014-2019.. ...
Background: Osteoarthritis (OA) is a destructive joint disease and there are no known biomarkers available for an early diagnosis. To identify potential disease biomarkers and gain further insight into the disease mechanisms of OA we applied quantitative proteomics with SILAC technology on the secretomes from chondrocytes of OA knees, designated as high Mankin (HM) scored secretome. A quantitative comparison was made between the secretomes of the medial and lateral femur condyle chondrocytes in the same knee since the medial femur condyle is usually more affected in OA than the lateral condyle, which was confirmed by Mankin scoring. The medial/lateral comparison was also made on the secretomes from chondrocytes taken from one individual with no clinically apparent joint-disease, designated as low Mankin (LM) scored secretome. Results: We identified 825 proteins in the HM secretome and 69 of these showed differential expression when comparing the medial and lateral femoral compartment. The LM ...
Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by ...
In Swiss 3T3 fibroblasts, long-term stimulation with PDGF, but not insulin-like growth factor 1 (IGF-1) or EGF, results in the establishment of an elongated migratory phenotype, characterized by the formation of retractile dendritic protrusions and absence of actin stress fibers and focal adhesion complexes. To identify receptor tyrosine kinase-specific reorganization of the Swiss 3T3 proteome during phenotypic differentiation, we compared changes in the pattern of protein synthesis and phosphorylation during long-term exposure to PDGF, IGF-1, EGF, and their combinations using 2DE-based proteomics after S-35- and P-33-metabolic labeling. One hundred and five differentially regulated proteins were identified by mass spectrometry and some of these extensively validated. PDGF stimulation produced the highest overall rate of protein synthesis at any given time and induced the most sustained phospho-signaling. Simultaneous activation with two or three of the growth factors revealed both synergistic ...
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Video created by Icahn School of Medicine at Mount Sinai for the course Experimental Methods in Systems Biology. Description goes here 2000+ courses from schools like Stanford and Yale - no application required. Build career skills in data ...
The Multiscale Imaging and Proteomics Core provides imaging of live animals, tissues, cells, and macromolecules coupled with protein characterization and quantitation services. The Core encompasses three umbrella technology thrusts: 1. Advanced multiscale imaging technology (headed by Dr. Ellisman); 2. Fluorescent reporters, indicators, and labels to monitor physiological and biochemical processes (headed by Dr. Tsien); and 3. Protein identification and quantitative proteomics (headed by Dr. Komives). This facility leverages the instrumentation and expertise of the National Center for Microscopy and Imaging Research (NCMIR) and the Biomolecular and Proteomics Mass Spectrometry Facility. These resources have been used to investigate the molecular mechanisms and the development of models that can be implemented to study the effects of exposure to superfund toxicants. The NCMIR is an NIH-supported National Biotechnology Research and Development Site, supported by NIH/NCRR and NIEHS. The NCMIR ...
This research focuses on (1) detection and Identification of microbes using mass spectrometry; (2) development of biological sample preparation methods compatible with mass spectrometry-based proteomic techniques; (3) development of detection and identification approaches of microbes using proteomics, metabolomics, and panomics approaches; and (4) development of bioinformatic algorithms using computational biology principles to enhance the reliable identification and taxonomic classification of microbes at various phylogenetic levels. ECBC is equipped with state-of-the-art instrumentation and facilities that will provide multidisciplinary research projects for recent postdoctoral graduate or other interested scientists.. References. Jabbour RE, et al: "Extracellular protein biomarkers for the characterization of enterohemorrhagic and enteroaggregative Escherichia coli strains." Journal of Microbiological Methods 98: 76-83, 2014. Jabbour RE, et al: Mass spectrometry for microbial proteomics." ...
The principal aim of Current Proteomics is to publish well-timed review articles in this fast-expanding area on topics relevant and significant to the development of proteomics. Current Proteomics is an essential journal for everyone involved in proteomics and related fields in both academia and industry.
Proteomics experiments typically involve protein or peptide separation steps coupled to the identification of many hundreds to thousands of peptides by mass spectrometry. Development of methodology and instrumentation in this field is proceeding rapidly, and effective software is needed to link the different stages of proteomic analysis. We have developed an application, proteogest, written in Perl that generates descriptive and statistical analyses of the biophysical properties of multiple (e.g. thousands) protein sequences submitted by the user, for instance protein sequences inferred from the complete genome sequence of a model organism. The application also carries out in silico proteolytic digestion of the submitted proteomes, or subsets thereof, and the distribution of biophysical properties of the resulting peptides is presented. proteogest is customizable, the user being able to select many options, for instance the cleavage pattern of the digestion treatment or the presence of modifications to
Soil salinity severely threatens land use capability and crop yields worldwide. An analysis of the molecular mechanisms of salt tolerance in halophytes will contribute to the development of salt-tolerant crops. In this study, a combination of physiological characteristics and iTRAQ-based proteomic approaches was conducted to investigate the molecular mechanisms underlying the salt response of suspension cell cultures of halophytic Halogeton glomeratus. These cells showed halophytic growth responses comparable to those of the whole plant. In total, 97 up-regulated proteins and 192 down-regulated proteins were identified as common to both 200 and 400 mM NaCl concentration treatments. Such salinity responsive proteins were mainly involved in energy, carbohydrate metabolism, stress defense, protein metabolism, signal transduction, cell growth, and cytoskeleton metabolism. Effective regulatory protein expression related to energy, stress defense, and carbohydrate metabolism play important roles in the salt
Mass spectrometry (MS) - based proteomics allows the sensitive and accurate quantification of almost complete proteomes of complex biological fluids and tissues. At the moment, however, the routinely usage of MS-based proteomics is prevented and complicated by the very complex work flow comprising sample preparation, chromatography, MS measurement followed by data processing and evaluation. The new technologies, products and assays developed by Precision Proteomics could help enabling and establishing mass spectrometry (MS) - based proteomics in academic and pharmaceutical proteomics research as well as in clinical diagnostics.. ...
Because there is little knowledge in the areas of stereocilia development, maintenance, and function in the hearing system, I decided to pursue a proteomics-based approach to discover proteins that play a role in stereocilia function. I employed a modified "twist-off" technique to isolate hair bundle proteins, and I developed a method to purify proteins and to process them for analysis using multi-dimensional protein identification technology (MudPIT). The MudPIT analysis yielded a substantial list of proteins. I verified the presence of 21 out of 34 (62%) existing proteins known to be present in stereocilia. This provided strong evidence that my proteomics approach was efficient in identifying hair bundle proteins. Next, I selected three proteins and localized them to murine cochlear stereocilia. StarD10, a putative phospholipid binding protein, was detectable along the shaft of stereocilia. Nebulin, a putative F-actin regulator, was located toward the base of stereocilia. Finally, twinfilin 2, ...
(EMAILWIRE.COM, November 16, 2017 ) Proteomics is the study of proteome which is a set of proteins present in the cell. Proteomes are different from one cell to another cell with requirements, stress, different time, and the organism. Proteomics help in the functioning and structure of the proteins...
Here, we describe a large-scale mass spectrometry-based proteomics approach to delineate phosphoproteome responses to the MEK inhibitor selumetinib in the context of KRAS-mutant lung cancer. Previous studies showed global phosphoproteome responses to MEK and RAF inhibition in the context of BRAF-mutant melanoma (48, 49); to our knowledge, this study is the first global phosphoproteomics approach that addresses how KRAS-mutant lung cancer cells respond to pharmacologic MEK inhibition. Importantly, we demonstrate widespread increases in protein phosphorylation following treatment with a MEK inhibitor, which at first glance seems counterintuitive. However, this result is consistent with other observations that kinase inhibitors can lead to increased phosphorylation of some substrate proteins. Previously, we revealed TBK1 knockdown leads to increased phosphorylation of EGFR, MET, and their downstream ERK→Jun, Myc in KRAS-mutant lung cancer cells (23). The tyrosine kinase inhibitor dasatinib ...
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets. Obstacles for comprehensive proteomic profiling include the immense size and structural heterogeneity of the proteome, and the broad range of abundance levels, as well. Proteome-wide, untargeted profiling can be performed in tissues and cells with tandem mass spectrometry. However, applications to plasma are limited by the need for complex preanalytical sample preparation stages ...
Health is a product of genome and exposome (food, microbiota, stress, exercise, pathogens): cells belonging to the same organism have the same genome, but the expression of genes is different and this affects the health or disease of the entire organism. Proteomics is the study of the levels of proteins expressed by genes and how these dynamically change in localization and over time, in response to perturbation. Proteomics enables the examination of how individual proteome profiles change during periods of health and disease, in high resolution. Proteomics, in correlation with other Personal Omics profiling methods such as microbiome, metabolomics and genomics, allows the discovery of unique therapies that treat an individuals disease based on their specific features.. ...
Read the current issue. Molecular & Cellular Proteomics is a monthly journal that seeks to foster the development and applications of proteomics in basic and translational research. MCP publishes biological or clinical discoveries underpinned by proteomic observations, and also emphasizes technological advances and innovative computational methods.. MCP leads the field in setting standards to promote reproducibility in proteomics research. The editorial board, in consultation with field-leading experts, has developed guidelines for data deposition and methodological description in these areas:. ...
Services offered by ProteoRed ProteoRed-ISCIII offers a broad range of services for the separation, identification, characterization and quantification of proteins and proteomes. These include the following techniques: Protein Identification Analysis of enzymatic protein digestions by using mass spectrometry (includes: sample preparation, digestion, clean up, data analysis) Protein Identification by LC/MS/MS (low to large scale) Protein identification by LC-MALDI (loew to large scale) Protein identification by PMF MS - MS/MS by MALDI TOF/TOF Protein Quantification Relative quantitation of differences in protein abundance by mass spectrometry (includes: sample preparation, labeling, digestion, clean up) Protein Quantification by LC-MSMS (label-free) Protein Quantification LC-MSMS (isobaric methods: TMT and iTRAQ) Protein Quantification LC-MSMS (metabolic labelling: SILAC) Protein Quantification LC-MSMS (isotopic methods: dimethyl, O18) Protein Quantification LC-MSMS (triple quadrupole, MRM ...
COLD SPRING HARBOR, N.Y. (Mon., Mar. 1, 2010) - The use of recombinant proteins, antibodies, small molecules, or nucleic acids as affinity reagents is a simple yet powerful strategy to study the protein/bait interactions that drive biological processes. Analysis via mass spectrometry rather than western blotting extends the identification of interactors, often allowing detection of thousands of proteins from complex mixtures. But this increased sensitivity can lead to problems distinguishing specific interactions from background noise. In the March issue of Cold Spring Harbor Protocols (www.cshprotocols.org/TOCs/toc3_10.dtl), Shao-En Ong from the Broad Institute of MIT and Harvard (www.broadinstitute.org/proteomics/team.html) presents Unbiased Identification of Protein/Bait Interactions Using Biochemical Enrichment and Quantitative Proteomics. This method uses quantitative proteomics approaches to compare enrichment with the bait of interest against samples using control baits to allow sensitive ...
Novel Imaging Mass Spectrometry-based Proteomics Technology to Identify Autism Biomarkers Autism spectrum disorders (ASD) are neurobehavioral syndromes with a prevalence of 1:68 in children. Evidence supports the hypothesis that, although pathogenetically different, ASD share common dysfunctional mechanisms and pathways which, unfortunately, remain largely unknown. We hypothesize that proteins and peptides which play a key role in the pathogenesis of autism demonstrate similar regional and age-dependent expression patterns in the brain in different syndromes of autism, and differ from those expressed in normal brains. Such proteins/peptides can be useful as biomarkers for early identification of individuals at risk for developing ASD, and some may even constitute novel therapeutic targets. We are exploring this hypothesis by combining novel high resolution proteomics methodologies and gene expression technology with behavioural, pharmacological and neuropathological studies in established mouse ...
Comparative Proteomics for Studying Muscular Dystrophy: Intrinsic Biological and Analytical Issues Associated with the Systematic Utilization of Tissue Specimens Abstract.
Comparative Proteomics Kit I: Protein Profiler Module. Protein Profiler Kit Instructors. Stan Hitomi Coordinator - Math & Science San Ramon Valley Unified School District Danville, CA Kirk Brown Lead Instructor, Edward Teller Education Center Science Chair, Tracy High School...
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed ...
Neuritic plaques comprised of amyloid ß (Aß) are one of the primary neuropathological hallmarks of Alzheimers disease (AD). However, Aß plaque deposition is preceded by aberrations of the endosomal/lysosomal system, including abnormally enlarged endosomal compartments, accumulation of protease-resistant proteins, and atypical activation of the lysosomal system. The functional mechanisms accounting for these abnormalities have not yet been delineated. Towards our goal of identifying the proteins whose dysfunction contributes to the development of endosomal/lysosomal pathology in AD, we have found that: 1) proteins implicated in regulating late endosomal trafficking are among the targets of oxidation (carbonylation) in the brain of a presenilin 1/amyloid precursor protein (PS1/APP) transgenic mouse model of AD; 2) reduced neuronal expression of synaptic membrane protein HNK-1/NCAM is associated with Aß pathology in models of Aß deposition in cell culture and an amyloid precursor protein ...
BRKR Bruker Corporation Bruker Announces Release of Breakthrough diaPASEF Workflow for CCS-aware 4D Proteomics on timsTOF™ Pro Platform at HUPO 201...
It is going to be more in-depth than anything Ill go into here -- and more in-depth than anything youll see from any commercial software package anytime soon. This review is partially so deep because this group at PNNL has a completely different idea of how we should be doing proteomics. In numerous studies they have shown that having high resolution accurate mass and accurate retention time is enough data to accurately do quantitative proteomics -- once you have a library of exact masses and retention times. And they have applied numerous statistical algorithms (some deriving from genomics techniques and others from pure statistics) to a few high quality data sets they have created to find the best ones -- and this is a wrap up of these. BTW, I LOVE these papers, I just dont think were quite there to applying these to the diseases I care about ...
Proteomic technologies in combination with pathway analysis promise to be of great value in molecular medicine, particularly for the discovery and validation of disease markers. Our biomarker detection efforts range from classical proteomics approaches such as quantitative mass spectrometry of brain tissue and body fluid proteins to in silico analyses of public data. A particular focus is the use of animal models that represent selected endophenotypes characteristic for the respective clinical psychiatric phenotype in humans. A comprehensive and sensitive proteomics platform that is based on metabolic labeling of mouse models with stable isotopes is used for mass spectrometry based analyses of protein levels and turnover. The resulting data can be used to detect disease relevant pathways and identify biosignatures that can be translated into the clinic. ...
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital in living organisms, as they are the main components of the physiological pathways of cells. The term "proteomics" was coined to make an analogy with genomics, the study of the genes. The proteome of an organism is the set of proteins produced by it during its life, and its genome is its set of genes. The proteome of a cell under a particular stimulation is the set of proteins in it. The word "proteome" derives from "proteins" and "genome", since proteins are expressed by the genome.. Proteomics is often considered the next step in the study of biological systems, after genomics. It is much more complicated than genomics, mostly because while an organisms genome is rather constant, a proteome differs from cell to cell and constantly changes through its biochemical interactions with the genome and the environment. One organism has radically different protein expression in different ...
Offline two-dimensional chromatography is a common means to achieve deep proteome coverage. To reduce sample complexity and dynamic range and to utilize mass spectrometer (MS) time efficiently, high chromatographic resolution of and good orthogonality between the two dimensions is needed. Ion exchange and high pH reversed phase chromatography are often used for this purpose. However, the former requires desalting to be MS-compatible and the latter requires fraction pooling to create orthogonality. Here, we report an alternative first-dimension separation technique using a commercial trimodal phase incorporating polar embedded reversed phase, weak anion exchange and strong cation exchange material. The column is capable of retaining polar and nonpolar peptides alike without noticeable breakthrough. It allows separating ordinary and TMT-labelled peptides under mild acidic conditions using an acetonitrile gradient. The direct MS compatibility of solvents and good orthogonality to online coupled C18 ...
Offline two-dimensional chromatography is a common means to achieve deep proteome coverage. To reduce sample complexity and dynamic range and to utilize mass spectrometer (MS) time efficiently, high chromatographic resolution of and good orthogonality between the two dimensions is needed. Ion exchange and high pH reversed phase chromatography are often used for this purpose. However, the former requires desalting to be MS-compatible and the latter requires fraction pooling to create orthogonality. Here, we report an alternative first-dimension separation technique using a commercial trimodal phase incorporating polar embedded reversed phase, weak anion exchange and strong cation exchange material. The column is capable of retaining polar and nonpolar peptides alike without noticeable breakthrough. It allows separating ordinary and TMT-labelled peptides under mild acidic conditions using an acetonitrile gradient. The direct MS compatibility of solvents and good orthogonality to online coupled C18 ...
Significance Analysis of INTeractome (SAINT) is a software package for scoring protein‐protein interactions based on label‐free quantitative proteomics data (e
Description of services, fees, forms and personnel for the Mass Spectrometry-Proteomics Core Laboratory at Baylor College of Medicine....
HeLa whole cell lysate (Positive control), 0.1 mg. This whole cell lysate is derived from a cell line or tissue using highly refined extraction protocols to ensure exceptionally high quality, protein integrity and lot-to-lot reproducibility.
Speckle-type POZ protein (SPOP) is an E3 ubiquitin ligase adaptor protein that functions as a potential tumor suppressor, and SPOP mutations have been identified in ~10% of human prostate cancers. However, it remains unclear if mutant SPOP proteins can be utilized as biomarkers for early detection, diagnosis, prognosis or targeted therapy of prostate cancer. Moreover, the SPOP mutation sites are distributed in a relatively short region with multiple lysine residues, posing significant challenges for bottom-up proteomics analysis of the SPOP mutations. To address this issue, PRISM (high-pressure, high-resolution separations coupled with intelligent selection and multiplexing)-SRM (selected reaction monitoring) mass spectrometry assays have been developed for quantifying wild-type SPOP protein and 11 prostate cancer-derived SPOP mutations. Despite inherent limitations due to amino acid sequence constraints, all the PRISM-SRM assays developed using Arg-C digestion showed a linear dynamic range of at least
Matrix-based reference materials such as serum and plasma address the need for assessment of temporal stability in instrumentation, optimization, and instrument performance and cross-platform comparisons to assess bias. A standardized, pooled serum or plasma preparation would address the majority of community needs for such a complex mixture. Although the volume of serum/plasma from one individual would be limited, plasma pools can supply aliquots linked to proteomic characterization measurements made on the pooled plasma. Homogeneous pooled samples also minimize individual differences in protein concentration. Because of potential interferences, however, pooled serum and plasma are not appropriate for research on autoantibodies. The concentrations of several known proteins in the pooled sera and plasma should be accurately determined and made available along with sample aliquots and documentation of technical details. Prior consensus documents on preparation of pools of human sera and plasma ...
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Cancer-associated fibroblasts (CAFs) play a central role in tumor progression through the mechanical remodeling of the stroma. Indeed CAFs secrete a plethora of extracellular matrix (ECM) components and ECM modifiers which contribute to generate stiff and dense tumors. Increased tumor stiffness induces endothelial cell (EC) sprouting and tumor cell invasion. Moreover, excessive stiffness represents a critical barrier to therapy because it blocks perfusion thus preventing diffusion of drugs and favoring hypoxia. Tuning tumor stiffness has therefore the potential to contribute to improve the efficacy of conventional anti-cancer therapies. Our study aims at using unbiased proteomics approach to identify CAF proteins which alter the tumor stroma, and investigating their functional role.. We have established mass spectrometry-based proteomics approach to accurately and in-depth analyze secretomes of cells in culture, and used it to compare cell lines of human mammary normal (iNF) and ...