Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most workflows require that such variations be included in the search space used to analyze the data, and doing so remains challenging with most analysis tools. In order to facilitate the search for known sequence variants and PTMs, the Proteomics Standards Initiative (PSI) has designed and implemented the PSI extended FASTA format (PEFF). PEFF is based on the very popular FASTA format but adds a uniform mechanism for encoding substantially more metadata about the sequence collection as well as individual entries, including support for encoding known sequence variants, PTMs, and proteoforms. The format is very nearly backward compatible, and as such, existing FASTA parsers will require little or no changes to be able to read PEFF files as FASTA files, although without supporting any of the
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 - Mass spectrometry in clinical proteomics - From the present to the future. AU - Palmblad, Magnus. AU - Tiss, Ali. AU - Cramer, Rainer. PY - 2009/5/14. Y1 - 2009/5/14. N2 - MS is an important analytical tool in clinical proteomics, primarily in the disease-specific discovery, identification and characterisation of proteomic biomarkers and patterns. MS-based proteomics is increasingly used in clinical validation and diagnostic method development. The latter departs from the typical application of MS-based proteomics by exchanging some of the high performance of analysis for the throughput, robustness and simplicity required for clinical diagnostics. Although conventional MS-based proteomics has become an important field in clinical applications, some of the most recent MS technologies have not yet been extensively applied in clinical proteomics. In this review, we will describe the current state of MS in clinical proteomics and look to the future of this field.. AB - MS is an ...
TY - JOUR. T1 - A liquid chromatography with tandem mass spectrometry-based proteomic analysis of cells cultured in DMEM 10% FBS and chemically defined medium using human adipose-derived mesenchymal stem cells. AU - Nakashima, Yoshiki. AU - Nahar, Saifun. AU - Miyagi-Shiohira, Chika. AU - Kinjo, Takao. AU - Kobayashi, Naoya. AU - Saitoh, Issei. AU - Watanabe, Masami. AU - Fujita, Jiro. AU - Noguchi, Hirofumi. PY - 2018/7/13. Y1 - 2018/7/13. N2 - Human adipose-derived mesenchymal stem cells (hADSCs) are representative cell sources for cell therapy. Classically, Dulbeccos Modified Eagles medium (DMEM) containing 10% fetal bovine serum (FBS) has been used as culture medium for hADSCs. A chemically defined medium (CDM) containing no heterologous animal components has recently been used to produce therapeutic hADSCs. However, how the culture environment using a medium without FBS affects the protein expression of hADSC is unclear. We subjected hADSCs cultured in CDM and DMEM (10% FBS) to a protein ...
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,
The Discovery Award in Proteomic Sciences has been awarded by the Human Proteome Organization (HUPO) to Albert J.R. Heck, Professor at the Science Faculty of Utrecht University. Heck is also scientific director of the Netherlands Proteomics Centre and coordinator of the European proteomics infrastructure PRIME-XS and the NWO roadmap funded Large-Scale Proteomics Research Facility Proteins At Work.. The Discovery in Proteomic Sciences award recognizes a scientist for an eminent single discovery in the field of proteomics. Heck receives the award because he has implemented innovative mass spectrometric methods with a unique emphasis on protein post-translational modifications and interactions.. Heck will receive the award during a ceremony at the HUPO World Congress in Yokohama, Japan, September 18, 2013.. Past award recipients are amongst others: Carol Robinson, Steve Carr, Matthias Mann, Catherine Costello, John Yates, Ruedi Aebersold and Brian Chait.. ...
Seminal fluid contains some of the fastest evolving proteins currently known. These seminal fluid proteins (Sfps) play crucial roles in reproduction, such as supporting sperm function, and particularly in insects, modifying female physiology and behavior. Identification of Sfps in small animals is challenging, and often relies on samples taken from the female reproductive tract after mating. A key pitfall of this method is that it might miss Sfps that are of low abundance because of dilution in the female-derived sample or rapid processing in females. Here we present a new and complementary method, which provides added sensitivity to Sfp identification. We applied label-free quantitative proteomics to Drosophila melanogaster, male reproductive tissue - where Sfps are unprocessed, and highly abundant - and quantified Sfps before and immediately after mating, to infer those transferred during copulation. We also analyzed female reproductive tracts immediately before and after copulation to confirm the
TY - JOUR. T1 - Differential expression proteomics of human colorectal cancer based on a syngeneic cellular model for the progression of adenoma to carcinoma. AU - Roth, U. AU - Razawi, H. AU - Hommer, J. AU - Engelmann, K. AU - Schwientek, T. AU - Müller, S. AU - Baldus, SE. AU - Patsos, G. AU - Corfield, AP. AU - Paraskeva, C. AU - Hanisch, FG. N1 - Publisher: Wiley. PY - 2010/1. Y1 - 2010/1. N2 - This is the first differential expression proteomics study on a human syngeneic cellular in vitro progression model of the colorectal adenoma-to-carcinoma sequence, the anchorage-dependent non-tumorigenic adenoma derived cell line AA/C1 and the derived anchorage-independent and tumorigenic carcinoma cell line AA/C1/SB10C. The study is based on quantitative 2-DE and is complemented by Western blot validation. Excluding redundancies due to proteolysis and post-translational modified isoforms of over 2000 protein spots, 13 proteins were revealed as regulated with statistical variance being within the ...
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 ...
Data Availability StatementThe mass spectrometry proteomics data have already been deposited towards the ProteomeXchange Consortium via the Satisfaction partner repository using the dataset identifier PXD002600 and 10. poorer inducing and result chemotherapy level of resistance in stable tumors. The unique trend of pseudo-hypoxia linked to mutation was seen in clear-cell, however, not in papillary RCC, and the treating this subtype of Wisp1 cancer is demanding continue to. Despite the intro of fresh antiangiogenic targeted treatments (tyrosine kinase inhibitors, TKIs), individuals develop both major and acquired level of resistance even now. Overcoming level of resistance to TKIs, in papillary RCC also, could be possible simply by finding modified protein expression considerably. To get this done, hypoxic 3D in vitro versions must be created to mimic both molecular pathways normal for low air pressure and cellCcell dynamics in tumor-like spatial constructions. Outcomes Clear-cell and papillary ...
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
Experimental strategies based on proteolytic digestion of protein mixtures introduce the complication of loss of connectivity between peptides and their protein precursors. Assignment of peptide sequences results in two outcomes; distinct peptides that map to only one protein sequence or shared peptides that map to more than one protein sequence. Detection of shared peptides introduces an uncertainty between the possibility that a shared peptide can be mapped to more than one protein sequence (bioinformatics redundancy) versus the possibility that more than one precursor is in the original protein mixture (physical redundancy). The apparent ambiguity in peptide assignment requires reporting of a protein group. When assembling peptides into proteins and protein groups, authors should adhere to principles of parsimony, i.e., describe the minimum set of protein sequences that adequately accounts for all observed peptides. While the identification of shared peptides implies that multiple related ...
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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The Proteomics Core Directors and Staff Symposium will emphasize new, cutting-edge technologies and approaches to discovery-phase proteomics that can be translated into practice at your home institution. Topics at the 2020 symposium will include experimental design for proteomics experiments, sample preparation and fractionation, human tissue proteomics, post-translational modifications, and top-down proteomics. Presentations will also cover non-scientific topics such as best business practices and core administration.. Keynote Address: TBA. To apply to attend the 2020 symposium, please complete the application form here. For more information on the symposium, please contact Sonet Smitherman ([email protected]).. Hosted by ...
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).
Research outputs, collaborations and relationships for Mass Spectrometry Proteomics, The Francis Crick Institute published between 1 December 2019 - 30 November 2020 as tracked by the Nature Index.
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 ...
Proteomic-Based Profiling of Lymphomas: Chromatin Proteomics; Composition and Modification of Histone and Non-Histone Chromosomal ...
Proteomic studies of respiratory disorders have the potential to identify protein biomarkers for diagnosis and disease monitoring. Utilisation of sensitive quantitative proteomic methods creates opportunities to determine individual patient proteomes. The aim of the current study was to determine if quantitative proteomics of bronchial biopsies from asthmatics can distinguish relevant biological functions and whether inhaled glucocorticoid treatment affects these functions. Endobronchial biopsies were taken from untreated asthmatic patients (n = 12) and healthy controls (n = 3). Asthmatic patients were randomised to double blind treatment with either placebo or budesonide (800 μg daily for 3 months) and new biopsies were obtained. Proteins extracted from the biopsies were digested and analysed using isobaric tags for relative and absolute quantitation combined with a nanoLC-LTQ Orbitrap mass spectrometer. Spectra obtained were used to identify and quantify proteins. Pathways analysis was performed
Proteomic studies of respiratory disorders have the potential to identify protein biomarkers for diagnosis and disease monitoring. Utilisation of sensitive quantitative proteomic methods creates opportunities to determine individual patient proteomes. The aim of the current study was to determine if quantitative proteomics of bronchial biopsies from asthmatics can distinguish relevant biological functions and whether inhaled glucocorticoid treatment affects these functions. Endobronchial biopsies were taken from untreated asthmatic patients (n = 12) and healthy controls (n = 3). Asthmatic patients were randomised to double blind treatment with either placebo or budesonide (800 μg daily for 3 months) and new biopsies were obtained. Proteins extracted from the biopsies were digested and analysed using isobaric tags for relative and absolute quantitation combined with a nanoLC-LTQ Orbitrap mass spectrometer. Spectra obtained were used to identify and quantify proteins. Pathways analysis was performed
TY - JOUR. T1 - Challenges and solutions in proteomics. AU - Huang, Hongzhan. AU - Shukla, Hem D.. AU - Wu, Cathy. AU - Saxena, Satya. PY - 2007/3. Y1 - 2007/3. N2 - The accelerated growth of proteomics data presents both opportunities and challenges. Large-scale proteomic profiling of biological samples such as cells, organelles or biological fluids has led to discovery of numerous key and novel proteins involved in many biological/disease processes including cancers, as well as to the identification of novel disease biomarkers and potential therapeutic targets. While proteomic data analysis has been greatly assisted by the many bioinformatics tools developed in recent years, a careful analysis of the major steps and flow of data in a typical high-throughput analysis reveals a few gaps that still need to be filled to fully realize the value of the data. To facilitate functional and pathway discovery for large-scale proteomic data, we have developed an integrated proteomic expression analysis ...
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.. ...
The Schey lab is interested in both method/instrument development in proteomics analysis as well as in applications of state-of-the-art proteomics technologies in the study of development and disease. Method development/technology projects include methods for integral membrane protein analysis, tandem mass spectrometry of intact proteins (top-down proteomics), spatially-resolved proteomics analysis, and quantitative proteomics. The major area of application is human lens protein modifications and protein-protein interactions. Other areas of interest are: proteomics analysis of heart valve development, and invertebrate (shrimp and oyster) innate immunity. Integral membrane proteins play key roles in signaling, transport, and adhesion, yet they remain difficult to analyze using conventional proteomics methods. Our lab has developed methods to analyze integral membrane proteins and membrane associated proteins including their modifications. In addition, we have developed methods for membrane proteome
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 ...
Dr. Hans Wessels specializes in translational clinical proteomics driving further development of emerging technologies contributing to healthcare. His professional career started as proteomics specialist at the Radboud University Medical Center in 2003 working on inborn errors of metabolism and biochemistry of novel microorganisms. In this time, he was key to establish the core proteomics facility of the Radboudumc. From 2010-2015, he performed his PhD research at the Nijmegen Center for Mitochondrial Disorders where he conceived and applied novel methods to study mitochondrial complexomes. Since then, he is building his own line of research on the importance of proteoforms in disease pathology at the Radboudumc Proteomics Center. Novel innovative projects include the development and implementation of Top-Down proteomics and Glycoproteomics for translational research and patient care. His track record includes over thirty publications in peer-reviewed journals, two book chapters, and he has been ...
We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein identification technology (MudPIT). MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date. A total of 1,484 proteins were detected and identified. Categorization of these hits demonstrated the ability of this technology to detect and identify proteins rarely seen in proteome analysis, including low-abundance proteins like transcription factors and protein kinases. Furthermore, we identified 131 proteins with three or more predicted transmembrane domains, which allowed us to map the soluble domains of many of the integral membrane proteins. MudPIT is useful for proteome analysis and may be specifically applied to integral membrane proteins to obtain detailed biochemical ...
Passing a kidney stone is painful and debilitating. In some patients kidney stones can result in kidney failure. Kidney stone disease affects around 10% of the population (1, 32, 33) worldwide and is increasing in prevalence (34). Epidemiologic studies have suggested that stone disease is linked to diet, fluid consumption, and obesity (30, 35-37), which impact both on kidney function and urinary composition. As a proximal fluid, with a simpler dynamic range than plasma, urine is particularly amenable to proteomic analysis for renal and urologic conditions. This is the first study to employ a comprehensive label-free platform to the urinary proteome of patients with urolithiasis. Among the differentially regulated proteins identified, ceruloplasmin, an acute phase copper binding metalloprotein, was validated independently in individual samples using ELISA. Ceruloplasmin also demonstrated a dose-dependent effect on calcium oxalate crystallization in vitro.. To date, few proteomics studies have ...
Seminal fluid contains some of the fastest evolving proteins currently known. These seminal fluid proteins (Sfps) play crucial roles in reproduction, such as supporting sperm function, and particularly in insects, modifying female physiology and behaviour. Identification of Sfps in small animals is challenging, and often relies on samples taken from the female reproductive tract after mating. A key pitfall of this method is that it might miss Sfps that are of low abundance due to dilution in the female derived sample or rapid processing in females. Here we present a new and complementary method, which provides added sensitivity to Sfp identification. We applied label-free quantitative proteomics to Drosophila melanogaster male reproductive tissue, where Sfps are unprocessed, and highly abundant, and quantified Sfps before and immediately after mating, to infer those transferred during copulation. We also analysed female reproductive tracts immediately before and after copulation to confirm the presence
Determining small molecule-target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition. Among 20 different bioorthogonal reactions, tetrazine ligation has been spotlighted as the most advanced bioorthogonal chemistry because of their extremely faster kinetics and higher specificity than others. Therefore, tetrazine ligation has a tremendous potential to enhance the proteomic research. This review highlights the current status of tetrazine ligation reaction as a molecular tool for the chemical
Determining small molecule-target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition. Among 20 different bioorthogonal reactions, tetrazine ligation has been spotlighted as the most advanced bioorthogonal chemistry because of their extremely faster kinetics and higher specificity than others. Therefore, tetrazine ligation has a tremendous potential to enhance the proteomic research. This review highlights the current status of tetrazine ligation reaction as a molecular tool for the chemical
Peptides are routinely identified from mass spectrometry-based proteomics experiments by matching observed spectra to peptides derived from protein databases. The error rates of these identifications can be estimated by target-decoy analysis, which involves matching spectra to shuffled or reversed peptides. Besides estimating error rates, decoy searches can be used by semi-supervised machine learning algorithms to increase the number of confidently identified peptides. As for all machine learning algorithms, however, the results must be validated to avoid issues such as overfitting or biased learning, which would produce unreliable peptide identifications. Here, we discuss how the target-decoy method is employed in machine learning for shotgun proteomics, focusing on how the results can be validated by cross-validation, a frequently used validation scheme in machine learning. We also use simulated data to demonstrate the proposed cross-validation schemes ability to detect overfitting.. ...
Title:iTRAQ-based Quantitative Proteomic Analysis of Dural Tissues Reveals Upregulated Haptoglobin to be a Potential Biomarker of Moyamoya Disease. VOLUME: 17 Author(s):Xiaojun Zhang, Lin Yin, Xiaofang Jia, Yujiao Zhang, Tiefu Liu and Lijun Zhang*. Affiliation:The 85th hospital of the Chinese Peoples Liberation Army, Shanghai 200052, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508. Keywords:Moyamoya disease, Dura mater, Proteomics, iTRAQ, Haptoglobin, Biomarker. Abstract:Background: Moyamoya disease (MMD) is a rare cerebrovascular disease with high rate of disability and mortality. Immune reactions has been implicated in the pathogenesis of MMD, however, the underlying ...
Peptide identification is an important problem in proteomics. One of the most popular scoring schemes for peptide identification is X-Corr (cross-correlation). Since calculating X-Corr is computationally intensive, a lot of efforts have been made to develop fast X-Corr engines. However, the existing X-Corr engines are not suitable for high-resolution MS/MS spectrometry because they are either slow or require a specific type of CPU. We present a portable high-speed X-Corr engine for high-resolution tandem mass spectrometry by developing a novel algorithm for calculating X-Corr. The algorithm enables X-Corr calculation 1.25-49 times faster than previous algorithms for 0.01 Da fragment tolerance. Furthermore, our engine is easily portable to any machine with different types of CPU because it is developed in C language. Hence, our X-Corr engine will expedite peptide identification by high-resolution tandem mass spectrometry ...
Helps researchers in proteomics and oncology work together to understand, prevent, and cure cancer. Proteomic data is increasingly important to understanding the origin and progression of cancer; however, most oncologic researchers who depend on proteomics for their studies do not collect the data themselves. As a result, there is a knowledge gap between scientists, who devise proteomic techniques and collect the data, and the oncologic researchers, who are expected to interpret and apply proteomic data. Bridging the gap between proteomics and oncology research, this book explains how proteomic technology can be used to address some of the most important questions in cancer research.. Proteomic Applications in Cancer Detection and Discovery enables readers to understand how proteomic data is acquired and analyzed and how it is interpreted. Author Timothy Veenstra has filled the book with examples many based on his own firsthand research experience that clearly demonstrate the application of ...
Title:Global Cell Proteome Profiling, Phospho-signaling and Quantitative Proteomics for Identification of New Biomarkers in Acute Myeloid Leukemia Patients. VOLUME: 17 ISSUE: 1. Author(s):Elise Aasebø, Rakel B. Forthun, Frode Berven, Frode Selheim and Maria Hernandez-Valladares. Affiliation:Department of Biomedicine, Faculty of Medicine, Building for Basic Biology, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.. Keywords:Acute myeloid leukemia, biomarker, mass spectrometry, proteomics, phosphoproteomics, diagnosis, prognosis.. Abstract:The identification of protein biomarkers for acute myeloid leukemia (AML) that could find applications in AML diagnosis and prognosis, treatment and the selection for bone marrow transplant requires substantial comparative analyses of the proteomes from AML patients. In the past years, several studies have suggested some biomarkers for AML diagnosis or AML classification using methods for sample preparation with low proteome coverage and low ...
Objective(s): Resistance to medications is one of the main complications in chemotherapy of cancer. It has been shown that some multidrug resistant cancer cells indicate more sensitivity against cytotoxic effects of TNF-α compared to their parental cells. Our previous findings indicated vulnerability of the mitoxantrone-resistant breast cancer cells MCF-7/MX to cell death induced by TNF-α compared to the parent cells MCF-7. In this study, we performed a comparative proteomics analysis for identification of proteins involved in induction of higher susceptibility of MCF-7/MX cells to cytotoxic effect of TNF-α.Materials and Methods: Intensity of protein spots in 2D gel electrophoresis profiles of MCF-7 and MCF-7/MX cells were compared with Image Master Platinum 6.0 software. Selected differential protein-spots were identified with MALDI-TOF/TOF mass spectrometry and database searching. Pathway analyses of identified proteins were performed using PANTHER, KEGG PATHWAY, Gene MANIA and STRING ...
MOTIVATION: We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates. RESULTS: We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable. AVAILABILITY AND IMPLEMENTATION: http://patternlabforproteomics.org/tdgc, freely available for academic use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
In this study, we had applied a comprehensive serum proteomics strategy to look for important differential proteins in serum based on AIH mouse model and patients serum. And totally 9 altered proteins were identified in AIH mice serum by 2-DE. Two upregulated proteins, C3 and A2M, were validated in the serum of AIH patients by a targeted iTRAQ analysis. And furthermore, serum level of C3 and A2M was generally higher in 34 cases of AIH patients than normal persons by ELISA detection. From mouse models to clinical AIH sera, the integrated serum proteomics investigation can overcome discrepancy in samples and tools, which is a translational medical viewpoint to look for the molecules associated with AIH.. Serum proteome contains the proteins not only from the liver, small intestine synthesis such as albumin, but also millions of species of immunoglobulin. The serum proteome holds the promise of a reform in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics ...
Macronutrients such as nitrogen (N), phosphorus (P), and silicon (Si) are essential for the productivity and distribution of diatoms in the ocean. Responses of diatoms to a particular macronutrient deficiency have been investigated, however, we know little about their common or specific responses to different macronutrients. Here, we investigated the physiology and quantitative proteomics of a diatom Thalassiosira pseudonana grown in nutrient-replete, N-, P-, and Si-deficient conditions. Cell growth was ceased in all macronutrient deficient conditions while cell volume and cellular C content under P- and Si-deficiencies increased. Contents of chlorophyll a, protein and cellular N decreased in both N- and P-deficient cells but chlorophyll a and cellular N increased in the Si-deficient cells. Cellular P content increased under N-and Si-deficiencies. Proteins involved in carbon fixation and photorespiration were down-regulated under all macronutrient deficiencies while neutral lipid synthesis and ...
TY - JOUR. T1 - A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. AU - Wolfe, Lisa M.. AU - Veeraraghavan, Usha. AU - Idicula-Thomas, Susan. AU - Schuerer, Stephan C. AU - Wennerberg, Krister. AU - Reynolds, Robert. AU - Besra, Gurdyal S.. AU - Dobos, Karen M.. PY - 2013/6/1. Y1 - 2013/6/1. N2 - Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the leading causes of death worldwide despite extensive research, directly observed therapy using multidrug regimens, and the widespread use of a vaccine. The majority of patients harbor the bacterium in a state of metabolic dormancy. New drugs with novel modes of action are needed to target essential metabolic pathways in M. tuberculosis; ATP-competitive enzyme inhibitors are one such class. Previous screening efforts for ATP-competitive enzyme inhibitors identified several classes of lead compounds that demonstrated potent anti-mycobacterial efficacy as well as tolerable levels of ...
TY - JOUR. T1 - Survey of the camel urinary proteome by shotgun proteomics using a multiple database search strategy. AU - Alhaider, Abdulqader A.. AU - Bayoumi, Nervana. AU - Argo, Evelyn. AU - Gader, Abdel G. M. A.. AU - Stead, David A.. PY - 2012/11. Y1 - 2012/11. N2 - We report the first survey of the dromedary camel urinary proteome. Proteins retained from ultrafiltration of urine were analysed by GeLC-MS/MS (SDS-PAGE followed by LC-MS/MS). In the absence of a complete camel genome sequence, the number of protein identifications was maximised by searching three primary sequence databases: Swiss-Prot, alpaca and camel EST. This search strategy enabled the identification of 1274 peptide sequences, of which 735 were found in at least two independent samples. Functional annotations for proteins identified from alpaca and camel EST sequences were mapped from basic local alignment search tool (protein) searches. These 735 peptides, which included many novel sequences found only in the camel EST ...
Corrigendum: Xylem Sap Proteomics Reveals Distinct Differences Between R Gene- and Endophyte-Mediated Resistance Against Fusarium Wilt Disease in Tomato Name of all authors as they appear in the published original article :Francisco J. de Lamo1, Maria E. Constantin1, David H. Fresno1, Sjef Boeren2, Martijn Rep1 and Frank L. W. Takken1*Affiliations of all authors as they appear in the published original version of the article 1Molecular Plant Pathology, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands2Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands* Correspondence: [email protected] Keywords: endophyte, biocontrol, Fusarium wilt disease, proteomics, NP24, PR-5x, exosomes Corrigendum on: de Lamo FJ, Constantin ME, Fresno DH, Boeren S, Rep M and Takken FLW (2018) Xylem Sap Proteomics Reveals Distinct Differences Between R Gene- and Endophyte-Mediated Resistance Against Fusarium Wilt Disease in Tomato. Front. Microbiol.
TY - JOUR. T1 - Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry. AU - Sidoli, Simone. AU - Fujiwara, Rina. AU - Kulej, Katarzyna. AU - Garcia, Benjamin A.. N1 - Publisher Copyright: © 2016 The Royal Society of Chemistry. Copyright: Copyright 2016 Elsevier B.V., All rights reserved.. PY - 2016. Y1 - 2016. N2 - Phosphorylation is a post-translational modification (PTM) fundamental for processes such as signal transduction and enzyme activity. We propose to apply data-independent acquisition (DIA) using mass spectrometry (MS) to determine unexplored phosphorylation events on isobarically modified peptides. Such peptides are commonly not quantitatively discriminated in phosphoproteomics due to their identical mass.. AB - Phosphorylation is a post-translational modification (PTM) fundamental for processes such as signal transduction and enzyme activity. We propose to apply data-independent acquisition (DIA) using mass spectrometry (MS) to ...
Fingerprint Dive into the research topics of High-throughput quantitative proteomic analysis of dengue virus type 2 infected A549 cells. Together they form a unique fingerprint. ...
The non-protein amino acid β-methylamino-L-alanine (BMAA) is a neurotoxin present in microalgae and shown to accumulate in the food web. BMAA has been linked to the complex neurodegenerative disorder of Guam and to increased incidents sporadic ALS. Two main neurotoxic routes are suggested; an excitotoxic by acting as an agonist towards glutamate receptors and a metabolic by misincorporating into cellular proteins. We have used zebrafish, an increasingly used model for neurodegenerative diseases, to further identify signaling components involved in BMAA-induced toxicity. Zebrafish embryos were exposed to sub-lethal dosages of BMAA and a label-free proteomics analysis was conducted on larvae 4 days post fertilization. The exposed larvae showed no developmental abnormalities, but a reduced heart rate and increased expression of GSK3 isoforms. Search towards a reviewed database containing 2968 entries identified 480 proteins. Only 17 of these were regulated 2-fold or more in the exposed larvae. ...
The small sample size was a limitation of our study. The SOMAscan we used measures 4001 proteins of the roughly 25,000 known human proteins. Because the focus was on the measured proteins in the pathway (see Supplementary File S1), rather than the pathways themselves containing an overrepresentation of significant proteins, the fact that we are not evaluating the entire proteome was lessened. A strength of the technology is the inclusion of low abundance proteins that are difficult to detect in other high-dimensional proteomic platforms. We feel we accomplished the objective of this small pilot study, which was to primarily determine the feasibility and potential usefulness of large-scale proteomics in AMD. Moreover, as a result of conducting this project we found some interesting associations of several proteins for neovascular AMD and GA. We chose to further illustrate the association with the top four proteins graphically but suggest that there may be other proteins worth pursuing in ...
Sodium Laurate, a Novel Protease- and Mass Spectrometry-Compatible Detergent for Mass Spectrometry-Based Membrane Proteomics. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Proteomics is a rapidly maturing field aimed at the high-throughput identification and quantification of all proteins in a biological system. The cornerstone of proteomic technology is tandem mass spectrometry of peptides resulting from the digestion of protein mixtures. The fragmentation pattern of each peptide ion is captured in its tandem mass spectrum, which enables its identification and acts as a fingerprint for the peptide. Spectral libraries are simply searchable collections of these fingerprints, which have taken on an increasingly prominent role in proteomic data analysis. This review describes the historical development of spectral libraries in proteomics, details the computational procedures behind library building and searching, surveys the current applications of spectral libraries, and discusses the outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:634-648, 2017.
Native proteomics aims to characterize complex proteomes under native conditions and ultimately produces a full picture of endogenous protein complexes in cells. It requires novel analytical platforms for high-resolution and liquid-phase separation of protein complexes prior to native mass spectrometry (MS) and MS/MS. In this work, size exclusion chromatography (SEC)-capillary zone electrophoresis (CZE)-MS/MS was developed for native proteomics in discovery mode, resulting in the identification of 144 proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli proteome. The protein complexes include four protein homodimers, 16 protein-metal complexes, two protein-[2Fe-2S] complexes, and one protein-glutamine complex. Half of them have not been reported in the literature. This work represents the first example of online liquid-phase separation-MS/MS for characterization of a complex proteome under the native condition, offering the proteomics community an efficient and simple ...
Proteomics International is proud to announce that it has received recognition for its continued export success in being admitted to the Western Australian Industry & Export Awards Hall of Fame.. Outstanding Western Australian businesses are bestowed each year with category awards by the Department of Jobs, Tourism, Science and Innovation. Proteomics International was presented with the Health & Biotechnology Award over the three years 2015, 2016, and 2018.. Proteomics International now joins other exceptional West Australian businesses in the Hall of Fame, a symbol of our continued commitment to industry and supporting the West Australian economy.. Read More: Winners of the 31st Western Australian Industry and Export Awards Announced. Video: Proteomics International enters Industry & Export Awards Hall of Fame. List of Hall of Fame Members. ...
Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox ...
The Human Proteome Project (HPP) is an international project organized by the Human Proteome Organization (HUPO) that aims to revolutionize our understanding of the human proteome via a coordinated effort by many research laboratories around the world. It is designed to map the entire human proteome in a systematic effort using currently available and emerging techniques. Completion of this project will enhance understanding of human biology at the cellular level and lay a foundation for development of diagnostic, prognostic, therapeutic, and preventive medical applications. ...
Schroecksnadel and collaborators seem a bit skeptical about our recent publication on β2 microglobulin (β2M)1 and about the laudatory editorial2 that accompanied it. Our article described the discovery that blood levels of β2M correlate with the severity of peripheral arterial disease (PAD) as assessed by the ankle-brachial index or treadmill testing. This novel finding arose from an agnostic high-throughput proteomic profiling effort using surface-enhanced laser desorption and ionization time-of-flight mass spectroscopy. This is a candidate-generating approach, in contrast to the more common candidate-based approach to proteomic profiling. The major advantage of the candidate-generating approach is that it provides for the discovery of new biomarkers for disease and potentially new insights into pathobiology. We hypothesized that repeated bouts of ischemia-reperfusion in the lower extremities could cause the expression and release of proteins that would be characteristic of the ischemic ...
The serine/threonine kinase mammalian target of rapamycin (mTOR) governs growth, metabolism, and aging in response to insulin and amino acids (aa), and is often activated in metabolic disorders and cancer. Much is known about the regulatory signaling network that encompasses mTOR, but surprisingly few direct mTOR substrates have been established to date. To tackle this gap in our knowledge, we took advantage of a combined quantitative phosphoproteomic and interactomic strategy. We analyzed the insulin- and aa-responsive phosphoproteome upon inhibition of the mTOR complex 1 (mTORC1) component raptor, and investigated in parallel the interactome of endogenous mTOR. By overlaying these two datasets, we identified acinus L as a potential novel mTORC1 target. We confirmed acinus L as a direct mTORC1 substrate by co-immunoprecipitation and MS-enhanced kinase assays. Our study delineates a triple proteomics strategy of combined phosphoproteomics, interactomics, and MS-enhanced kinase assays for the de ...
Proteomic platforms have gained increasing attention in the clinical spectrum of nonalcoholic fatty liver disease (NAFLD). This approach allows for the unbiased discovery of circulating biochemical markers, i.e., it is not limited to known molecules of presumed importance. This manuscript provides an overview of proteomic serum biomarker discovery in NAFLD. Hemoglobin is currently the most widely replicated proteomic circulating biomarker of NAFLD; it was identified as a biomarker of fatty liver in two distinct proteomic studies and subsequently validated using distinct analytical methods by independent research groups in large replication cohorts. Given the increasing availability of numerous serum samples and the refinement of the technological platforms available to scrutinize the blood proteome, large collaborative studies between academia and industry are warmly encouraged to identify novel, unbiased circulating biomarkers of NAFLD. (C) 2012 Elsevier B.V. All rights reserved. ...
Despite the success of tamoxifen since its introduction, about one-third of patients with estrogen (ER) and/or progesterone receptor (PgR) - positive breast cancer (BC) do not benefit from therapy. Here, we aim to identify molecular mechanisms and protein biomarkers involved in tamoxifen resistance. Using iTRAQ and Immobilized pH gradient-isoelectric focusing (IPG-IEF) mass spectrometry based proteomics we compared tumors from 12 patients with early relapses (|2 years) and 12 responsive to therapy (relapse-free | 7 years). A panel of 13 proteins (TCEAL4, AZGP1, S100A10, ALDH6A1, AHNAK, FBP1, S100A4, HSP90AB1, PDXK, GFPT1, RAB21, MX1, CAPS) from the 3101 identified proteins, potentially separate relapse from non-relapse BC patients. The proteins in the panel are involved in processes such as calcium (Ca2+) signaling, metabolism, epithelial mesenchymal transition (EMT), metastasis and invasion. Validation of the highest expressed proteins in the relapse group identify high tumor levels of CAPS as
Has, Canan; Mungan, Mehmet Direnc; Allmer, Jens] Izmir Inst Technol, Mol Biol & Genet, Izmir, Turkey; [Has, Canan; Allmer, Jens] Bionia Inc, IZTEKGEB A8, Izmir, Turkey; [Ciftci, Cansu] Izmir Inst Technol, Biotechnol, Izmir, ...
A Periodate-Cleavable Linker for Functional Proteomics under Slightly Acidic Conditions: Application for the Analysis of Intracellular Aspartic ...
A crucial aim upon the completion of the human genome is the verification and functional annotation of all predicted genes and their protein products. Here we describe the mapping of peptides derived from accurate interpretations of protein tandem mass spectrometry (MS) data to eukaryotic genomes and the generation of an expandable resource for integration of data from many diverse proteomics experiments. Furthermore, we demonstrate that peptide identifications obtained from high-throughput proteomics can be integrated on a large scale with the human genome. This resource could serve as an expandable repository for MS-derived proteome information.
Fibroblasts are mesenchymal stromal cells which occur in all tissue types. While their main function is related to ECM production and physical support, they are also important players in wound healing, and have further been recognized to be able to modulate inflammatory processes and support tumor growth. Fibroblasts can display distinct phenotypes, depending on their tissue origin, as well as on their functional state. In order to contribute to the proteomic characterization of fibroblasts, we have isolated primary human fibroblasts from human skin, lung and bone marrow and generated proteome profiles of these cells by LC-MS/MS. Comparative proteome profiling revealed characteristic differences therein, which seemed to be related to the cells tissue origin. Furthermore, the cells were treated in vitro with the pro-inflammatory cytokine IL-1beta. While all fibroblasts induced the secretion of Interleukins IL-6 and IL-8 and the chemokine GRO-alpha, other inflammation-related proteins were up-regulated
Background: The immense diagnostic potential of human plasma has prompted great interest and effort in cataloging its contents, exemplified by the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) pilot project. Due to challenges in obtaining a reliable blood plasma protein list, HUPO later re-analysed their own original dataset with a more stringent statistical treatment that resulted in a much reduced list of high confidence (at least 95%) proteins compared with their original findings. In order to facilitate the discovery of novel biomarkers in the future and to realize the full diagnostic potential of blood plasma, we feel that there is still a need for an ultra-high confidence reference list (at least 99% confidence) of blood plasma proteins. Methods: To address the complexity and dynamic protein concentration range of the plasma proteome, we employed a linear ion-trap-Fourier transform (LTQ-FT) and a linear ion trap-Orbitrap (LTQ-Orbitrap) for mass spectrometry (MS) ...
Abstract. Proteomics was thought to be a natural extension after the field of genomics has deposited significant amount of data. However, simply taking a straight verbatim approach to catalog all proteins in all tissues of different organisms is not viable. Researchers may need to focus on the perspectives of proteomics that are essential to the functional outcome of the cells. In Integrative Proteomics, expert researchers contribute both historical perspectives, new developments in sample preparation, gel-based and non-gel-based protein separation and identification using mass spectrometry. Substantial chapters are describing studies of the sub-proteomes such as phosphoproteome or glycoproteomes which are directly related to functional outcomes of the cells. Structural proteomics related to pharmaceutics development is also a perspective of the essence. Bioinformatics tools that can mine proteomics data and lead to pathway analyses become an integral part of proteomics. Integrative proteomics ...
Meet leading proteomics researchers, scientists, bioinformaticians & health care professionals at proteomics conferences, congress, workshops, events, meetings from human proteome organization, societies, associations during 2018, 2017 at paris, rome, valencia, London, Vienna
College of Life Sciences and Agriculture Department of Cellular, Molecular and Biomedical Sciences Tenure-Track Position in Proteomics The newly-formed Department of Cellular, Molecular and Biomedical Sciences seeks to fill a tenure-track position in Proteomics. The ideal candidate will use a proteomics approach to address questions in any area of biology (e.g. human health, agriculture, environmental or basic cellular biology). The proteomics position will be housed in the Hubbard Center for Genome Studies and join existing research groups in genomics and glycomics with a strong commitment to interdisciplinary research and teaching. Appointment may be at any level. The successful applicant will have a strong publication record, demonstrate the ability to develop/maintain a vigorous independent research program and actively participate in training of students at all levels. For more information go to: http://www.colsa.unh.edu/employment/ The University of New Hampshire is a high research ...
A Senior Research Scientist position focusing on quantitative proteomics is available at the Mass Spectrometry Facility at the University of Massachusetts Medical School. Affiliated with the Department of Biochemistry and Molecular Pharmacology, the Facility supports projects in basic and translational science across a diverse range of applications in proteomics, structural biology, metabolomics, small molecule quantitation, and mass spectrometry imaging. There are nine mass spectrometry platforms including four Orbitraps (Thermo Fusion Lumos w/ ETD and FAIMS, Q Exactive HF-X, Q Exactive and Orbitrap Velos Pro), a Q-TOF (Waters Synapt G2-Si) and two triple quadrupoles (Waters Xevo TQ-XS and Thermo TSQ Quantiva), all located in a spacious 5,000 sq. ft facility. This is a unique growth opportunity for an enthusiastic self-starter that will contribute to a wide and diverse range of projects both within the University of Massachusetts and to the external scientific community at large. The individual ...
400 Quantitative proteome analysis of tongue squamous cell carcinoma was performed by using laser capture microdissection (LCM) and mass spectrometry. LCM allowed for the one-step procurement of homogeneous populations of normal/tumor epithelial cells from tissue sections. The protein expression profiles of dissected normal/cancer cells were examined using a quantitative proteomics approach based on stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS). Both protein extracts were reduced, alkylated and digested with trypsin. The resulting peptides were labeled with iTRAQ 114 and 117 reagents, respectively. Both labeled peptides were then combined and analyzed simultaneously by nanoflow LC-QTOF MS for protein identification and quantitation. A total of 115 proteins were found to be differentially expressed, including 37 up-regulated (1.2-3 fold change) and 78 down-regulated (1.2-4 fold change) proteins in human tongue cancer tissue. A number of proteins altered at their ...
Brief Description of Core: The Upstate Proteomics & Mass Spectrometry Core Facility offers Upstate (and external) researchers cutting edge technology to support research projects involving proteomics or metabolomics applications. The facility is equipped with a state-of-the-art Thermo LTQ Orbitrap mass spectrometer for superior sensitivity and resolution that allows the identification and quantification of complex mixtures of proteins or metabolites.. More information on services, fees, and sample preparation can be found on the Proteomics & Mass Spectrometry Core Facility website.. ...
This course will discuss details of the statistical experimental design of quantitative mass spectrometry-based proteomic experiments, and the analysis of the acquired data with multiple data processing tools in MSstats. The topics include normalization, principles of statistical inference, summarization of protein abundances from multiple spectral features, derivation of confidence intervals for fold changes, testing proteins for differential abundance, and multivariate analysis for discovery of biomarker. The participants will perform hands-on analyses of the example datasets with open-source software R, MSstats, and other packages.. ...
The utility of four types of Ciphergen Protein Chips were evaluated by comparing protein profiles in control, and in in vitro acrylamide or glycidamide exposed urine using Surface Enhanced Laser Desorption Ionization Time of Flight (SELDI-TOF) mass spectrometry. Acrylamide (CAS 79-06-1), a widely used industrial chemical, which also may be formed in thermally processed food, can produce peripheral
Discovery proteomics is a good starting point to evaluate the feasability of a project and to further design an analytical strategy.. It is the method of choice for proteome mapping and identification of PTMs.. We can deploy tailor-made analytical methods that meet the needs of your project. Relative quantification between samples is possible.. Applications that require discovery analysis. ...
Connie R. Jimenez, Ph.D. is head of the OncoProteomics Laboratory and Associate Professor at the Dept. Medical Oncology of the VU University Medical Center in Amsterdam, The Netherlands. She is a biologist with an interest in disease pathway and biomarker discovery in cancer and neurodegenerate disease. She has a wide experience with biological and clinical applications of mass spectrometry. Het lab focuses on label-free mass spectrometry-based proteomics as a tool to address a range of biomedical and translational research questions ...
Streptococcus pyogenes is a major bacterial pathogen and a potent inducer of inflammation causing plasma leakage at the site of infection.