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low-throughput proteomics

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https://read.qxmd.com/read/30841911/seasonal-variation-in-equine-follicular-fluid-proteome
#1
G A Dutra, G M Ishak, O Pechanova, T Pechan, D G Peterson, J C F Jacob, S T Willard, P L Ryan, E L Gastal, J M Feugang
BACKGROUND: Proteomic studies of follicular fluid (FF) exist for several species, including the horse; however, the seasonal influence on FF proteome has not been explored in livestock. The application of high-throughput proteomics of FF in horse has the potential to identify seasonal variations of proteins involved in follicle and oocyte growth. METHODS: This study (i) profiles the proteomes of equine FF collected from dominant growing follicles during the spring anovulatory season (SAN), and spring (SOV), summer (SUM), and fall (FOV) ovulatory seasons; and (ii) identifies season-dependent regulatory networks and associated key proteins...
March 6, 2019: Reproductive Biology and Endocrinology: RB&E
https://read.qxmd.com/read/30826357/proteomics-based-identification-of-kdm5-histone-demethylases-associated-with-cardiovascular-disease
#2
Marika Mokou, Julie Klein, Manousos Makridakis, Vasiliki Bitsika, Jean-Loup Bascands, Jean Sebastien Saulnier-Blache, William Mullen, Michael Sacherer, Jerome Zoidakis, Burkert Pieske, Harald Mischak, Maria G Roubelakis, Joost P Schanstra, Antonia Vlahou
BACKGROUND: The increased prevalence of cardiovascular disease (CVD) indicates a demand for novel therapeutic approaches. Proteome analysis of vascular tissues from animal models and humans with CVD could lead to the identification of novel druggable targets. METHODS: LC-MS/MS analysis of thoracic aortas from three mouse models of non-diabetic and diabetic (streptozotocin (STZ)-induced) atherosclerosis followed by bioinformatics/pathway analysis was performed. Selected findings were confirmed by proteomics analysis of human vessels from patients with CVD as well as in vitro studies (migration, proliferation, angiogenesis assays) using endothelial (HUVEC) cells...
February 27, 2019: EBioMedicine
https://read.qxmd.com/read/30820711/meeting-the-challenge-of-developing-food-crops-with-improved-nutritional-quality-and-food-safety-leveraging-proteomics-and-related-omics-techniques
#3
REVIEW
Shalu Jain, Anjana Rustagi, Deepak Kumar, Mohd Aslam Yusuf, Shashi Shekhar, Neera Bhalla Sarin
Eliminating malnutrition remains an imminent priority in our efforts to achieve food security and providing adequate calories, proteins, and micronutrients to the growing world population. Malnutrition may be attributed to socio-economic factors (poverty and limited accessibility to nutritional food), dietary preferences, inherent nutrient profiles of traditional food crops, and to a combination of all such factors. Modern advancements in "omics" technology have made it possible to reliably predict, diagnose, and suggest ways to remedy the low protein content and bioavailability of key micronutrients in food crops...
February 28, 2019: Biotechnology Letters
https://read.qxmd.com/read/30755102/microrna-143-is-associated-with-pathological-complete-response-and-regulates-multiple-signaling-proteins-in-breast-cancer
#4
Raúl García-Vázquez, Laurence A Marchat, Erika Ruíz-García, Horacio Astudillo-de la Vega, Abelardo Meneses-García, Claudia Arce-Salinas, Enrique Bargallo-Rocha, Ángeles Carlos-Reyes, José Sullivan López-González, Carlos Pérez-Plasencia, Rosalío Ramos-Payán, Maribel Aguilar-Medina, César López-Camarillo
Almost 55% to 80% of patients with breast cancer have an unfavorable pathological complete response to chemotherapy. MicroRNAs are small noncoding RNAs involved in cancer progression; however, their utility as predictors of pathological complete response to neoadjuvant chemotherapy is unclear. Here, we investigated if miR-143 could discriminate between pathological complete response and no-polymerase chain reaction of patients with locally advanced triple negative breast cancer that have received a fluorouracil-cisplatin/paclitaxel-based neoadjuvant treatment...
January 1, 2019: Technology in Cancer Research & Treatment
https://read.qxmd.com/read/30699290/detecting-secretory-proteins-by-acoustic-droplet-ejection-in-multiplexed-high-throughput-applications
#5
Michael J Iannotti, Ryan MacArthur, Richard Jones, Dingyin Tao, Ilyas Singeç, Sam Michael, James Inglese
Nearly one-third of the encoded proteome is comprised of secretory proteins that enable communication between cells and organ systems, playing a ubiquitous role in human health and disease. High-throughput detection of secreted proteins would enhance efforts to identify therapies for secretion-related diseases. Using the Z mutant of alpha-1 antitrypsin as a human secretory model, we have developed 1536-well high-throughput screening assays that utilize acoustic droplet ejection to transfer nanoliter volumes of sample for protein quantification...
February 14, 2019: ACS Chemical Biology
https://read.qxmd.com/read/30679258/investigating-lactococcus-lactis-mg1363-response-to-phage-p2-infection-at-the-proteome-level
#6
Marie-Laurence Lemay, Andreas Otto, Sandra Maaß, Kristina Plate, Dörte Becher, Sylvain Moineau
Phages are viruses that specifically infect and eventually kill their bacterial hosts. Bacterial fermentation and biotechnology industries see them as enemies, however, they are also investigated as antibacterial agents for the treatment or prevention of bacterial infections in various sectors. They also play key ecological roles in all ecosystems. Despite decades of research some aspects of phage biology are still poorly understood. In this study, we used label-free quantitative proteomics to reveal the proteotypes of Lactococcus lactis MG1363 during infection by the virulent phage p2, a model for studying the biology of phages infecting Gram-positive bacteria...
January 24, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30630436/in-vitro-chondrogenic-potency-of-surplus-chondrocytes-from-autologous-transplantation-procedures-does-not-predict-short-term-clinical-outcomes
#7
Ashraful Islam, Vegard Fossum, Ann Kristin Hansen, Ilona Urbarova, Gunnar Knutsen, Inigo Martinez-Zubiaurre
BACKGROUND: Autologous chondrocyte implantation (ACI) has been used over the last two decades to treat focal cartilage lesions aiming to delay or prevent the onset of osteoarthritis; however, some patients do not respond adequately to the procedure. A number of biomarkers that can forecast the clinical potency of the cells have been proposed, but evidence for the relationship between in vitro chondrogenic potential and clinical outcomes is missing. In this study, we explored if the ability of cells to make cartilage in vitro correlates with ACI clinical outcomes...
January 10, 2019: BMC Musculoskeletal Disorders
https://read.qxmd.com/read/30612793/symposium-review-characterization-of-the-bovine-milk-protein-profile-using-proteomic-techniques
#8
Sabrina L Greenwood, Mallory C Honan
Identification and characterization of the comprehensive bovine milk proteome has historically been limited due to the dichotomy of protein abundances within milk. The high abundance of a select few proteins, including caseins, α-lactalbumin, β-lactoglobulin, and serum albumin, has hindered intensive identification and characterization of the vast array of low-abundance proteins in milk due to limitations in separation techniques and protein labeling capacity. In more recent years, the development and advancement of proteomics techniques have yielded valuable tools for characterization of the protein profile in bovine milk...
January 3, 2019: Journal of Dairy Science
https://read.qxmd.com/read/30608134/hotmaq-a-multiplexed-absolute-quantification-method-for-targeted-proteomics
#9
Xiaofang Zhong, Qinying Yu, Fengfei Ma, Dustin C Frost, Lei Lu, Zhengwei Chen, Henrik Zetterberg, Cynthia M Carlsson, Ozioma Okonkwo, Lingjun Li
Absolute quantification in targeted proteomics is challenging due to a variety of factors, including low specificity in complex backgrounds, limited analytical throughput, and wide dynamic range. To address these problems, we developed a hybrid offset-triggered multiplex absolute quantification (HOTMAQ) strategy that combines cost-effective mass difference and isobaric tags to enable simultaneous construction of an internal standard curve in the MS1 precursor scan, real-time identification of peptides at the MS2 level, and mass offset-triggered accurate quantification of target proteins in synchronous precursor selection (SPS)-MS3 spectra...
January 4, 2019: Analytical Chemistry
https://read.qxmd.com/read/30577643/integrating-multiple-interaction-networks-for-gene-function-inference
#10
Jingpu Zhang, Lei Deng
In the past few decades, the number and variety of genomic and proteomic data available have increased dramatically. Molecular or functional interaction networks are usually constructed according to high-throughput data and the topological structure of these interaction networks provide a wealth of information for inferring the function of genes or proteins. It is a widely used way to mine functional information of genes or proteins by analyzing the association networks. However, it remains still an urgent but unresolved challenge how to combine multiple heterogeneous networks to achieve more accurate predictions...
December 21, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://read.qxmd.com/read/30550622/a-review-of-lifestyle-metabolic-risk-factors-and-blood-based-biomarkers-for-early-diagnosis-of-pancreatic-ductal-adenocarcinoma
#11
REVIEW
Yuanjie Pang, Michael V Holmes, Zhengming Chen, Christiana Kartsonaki
We aimed to review the epidemiologic literature examining lifestyle, metabolic risk factors, and blood-based biomarkers including multi-omics (genomics, proteomics, and metabolomics) and to discuss how these predictive markers can inform early diagnosis of pancreatic ductal adenocarcinoma (PDAC). A search of the PubMed database was conducted in June 2018 to review epidemiologic studies of (1) lifestyle and metabolic risk factors for PDAC, genome-wide association studies (GWAS), and risk prediction models incorporating these factors and (2) blood-based biomarkers for PDAC (conventional diagnostic markers, metabolomics, and proteomics)...
December 14, 2018: Journal of Gastroenterology and Hepatology
https://read.qxmd.com/read/30523691/a-tandem-mass-spectrometry-sequence-database-search-method-for-identification-of-o-fucosylated-proteins-by-mass-spectrometry
#12
Kristian E Swearingen, Jimmy K Eng, David Shteynberg, Vladimir Vigdorovich, Timothy A Springer, Luis Mendoza, Noah D Sather, Eric W Deutsch, Stefan H I Kappe, Robert L Moritz
Thrombospondin type 1 repeats (TSRs), small adhesive protein domains with a wide range of functions, are usually modified with O-linked fucose, which may be extended to O-fucose-β1,3-glucose. Collision-induced dissociation (CID) spectra of O-fucosylated peptides cannot be sequenced by standard tandem mass spectrometry (MS/MS) sequence database search engines because O-linked glycans are highly labile in the gas phase and are effectively absent from the CID peptide fragment spectra, resulting in a large mass error...
December 7, 2018: Journal of Proteome Research
https://read.qxmd.com/read/30500165/selective-enrichment-and-quantification-of-n-terminal-glycine-peptides-via-sortase-a-mediated-ligation
#13
Ting Cao, Jing Lv, Lei Zhang, Guoquan Yan, Haojie Lu
The identification and quantification of low abundant proteins are always impeded by high abundant proteins in proteomic analysis because of the extreme complexity of peptide mixtures and wide dynamic range of protein abundances. Here, we developed a novel approach to enrich and quantify N-terminal glycine peptides through sortase A mediated ligation. This strategy was based on the formation of a covalent bond between the sortase A recognition motif LPXTG and a N-terminal glycine residue. And the quantification was achieved by introducing isotopically labelled threonine in the motif LPXTG...
November 30, 2018: Analytical Chemistry
https://read.qxmd.com/read/30485817/quantitative-proteomics-evaluation-of-human-multipotent-stromal-cell-for-%C3%AE-cell-regeneration
#14
Miljan Kuljanin, Ruth M Elgamal, Gillian I Bell, Dimetri Xenocostas, Anargyros Xenocostas, David A Hess, Gilles A Lajoie
Human multipotent stromal cells (hMSCs) are one of the most versatile cell types used in regenerative medicine due to their ability to respond to injury. In the context of diabetes, it has been previously shown that the regenerative capacity of hMSCs is donor specific after transplantation into streptozotocin (STZ)-treated immunodeficient mice. However, in vivo transplantation models to determine regenerative potency of hMSCs are lengthy, costly, and low throughput. Therefore, a high-throughput quantitative proteomics assay was developed to screen β cell regenerative potency of donor-derived hMSC lines...
November 27, 2018: Cell Reports
https://read.qxmd.com/read/30465509/nmr-based-metabolomics-an-exquisite-and-facile-method-for-evaluating-therapeutic-efficacy-and-screening-drug-toxicity
#15
Anupam Guleria, Amit Kumar, Umesh Kumar, Ritu Raj, Dinesh Kumar
Metabolomics is an analytical approach to metabolism and involves quantitative and comparative analysis of low-molecular-weight metabolites in body fluids or cellular/tissues extracts. Owing to its ability to reveal disease-specific metabolic patterns or metabolic changes produced in response to a therapeutic intervention; it is gaining widespread applications virtually in all aspects of biomedical and pharmaceutical research pertaining to human healthcare management. It has also started playing a strategic role in pharmacological and toxicological research for evaluating therapeutic efficacy/safety of promising drug candidates either alone or in conjunction with other omics tools such as genomics, transcriptomics and proteomics...
November 20, 2018: Current Topics in Medicinal Chemistry
https://read.qxmd.com/read/30463841/development-and-validation-of-apolipoprotein-ai-associated-lipoprotein-proteome-panel-for-the-prediction-of-cholesterol-efflux-capacity-and-coronary-artery-disease
#16
Zhicheng Jin, Timothy S Collier, Darlene L Y Dai, Virginia Chen, Zsuzsanna Hollander, Raymond T Ng, Bruce M McManus, Robert Balshaw, Sophia Apostolidou, Marc S Penn, Cory Bystrom
BACKGROUND: Cholesterol efflux capacity (CEC) is a measure of HDL function that, in cell-based studies, has demonstrated an inverse association with cardiovascular disease. The cell-based measure of CEC is complex and low-throughput. We hypothesized that assessment of the lipoprotein proteome would allow for precise, high-throughput CEC prediction. METHODS: After isolating lipoprotein particles from serum, we used LC-MS/MS to quantify 21 lipoprotein-associated proteins...
November 21, 2018: Clinical Chemistry
https://read.qxmd.com/read/30462917/assessing-automated-sample-preparation-technologies-for-high-throughput-proteomics-of-frozen-well-characterized-tissues-from-swedish-biobanks
#17
Magdalena Kuras, Lazaro Hiram Betancourt, Melinda Rezeli, Jimmy Rodriguez, Marcell Szasz, Qimin Zhou, Tasso Miliotis, Roland Andersson, György Marko-Varga
Large cohorts of carefully collected clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such large sample cohorts requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors and low reproducibility. In this work, three automated technologies for high-throughput proteomics of frozen sectioned tissues were compared...
November 21, 2018: Journal of Proteome Research
https://read.qxmd.com/read/30460336/comparative-characterization-of-osteoclasts-derived-from-murine-bone-marrow-macrophages-and-raw-264-7-cells-using-quantitative-proteomics
#18
Andrew Yh Ng, Chengjian Tu, Shichen Shen, Ding Xu, Merry J Oursler, Jun Qu, Shuying Yang
Osteoclasts are bone-resorbing cells differentiated from macrophage/monocyte precursors in response to macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-κB ligand (RANKL). In vitro models are principally based on primary bone marrow macrophages (BMMs), but RAW 264.7 cells are frequently used because they are widely available, easy to culture, and more amenable to genetic manipulation than primary cells. Increasing evidence, however, has shown that the vastly different origins of these two cell types may have important effects on cell behavior...
November 2018: JBMR Plus
https://read.qxmd.com/read/30319591/deciphering-the-interactome-of-neisseria-meningitidis-with-human-brain-microvascular-endothelial-cells
#19
Evelína Kánová, Irene Jiménez-Munguía, Petra Majerová, Zuzana Tkáčová, Katarína Bhide, Patrícia Mertinková, Lucia Pulzová, Andrej Kováč, Mangesh Bhide
Neisseria meningitidis is able to translocate the blood-brain barrier and cause meningitis. Bacterial translocation is a crucial step in the onset of neuroinvasion that involves interactions between pathogen surface proteins and host cells receptors. In this study, we applied a systematic workflow to recover and identify proteins of N. meningitidis that may interact with human brain microvascular endothelial cells (hBMECs). Biotinylated proteome of N. meningitidis was incubated with hBMECs, interacting proteins were recovered by affinity purification and identified by SWATH-MS...
2018: Frontiers in Microbiology
https://read.qxmd.com/read/30295461/dia-a-data-independent-acquisition-method-combining-multiple-precursor-charges-to-improve-peptide-signal
#20
Eva Borràs, Eduard Sabidó
Data-independent acquisition methods that acquire fragment ions from virtually any peptide in a sample have expanded the benefits of low-throughput targeted proteomics to proteome-wide analyses. While these methods have increased the reproducibility of peptide quantification across multiple samples, their sensitivity is still limited, and the quantification of complete proteomes remains a challenge. Here we present DIA+, a DIA method that combines signals from identical peptides with different charge states, resulting in improved signal-to-noise, additional number of fragments, and therefore in a higher number of identified and quantified peptides in complex samples...
November 6, 2018: Analytical Chemistry
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