Journal articles: 'Low-abundance proteome'

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Zhang, Hui. "The Plasma Proteome: High Abundance versus Low Abundance." Expert Review of Proteomics 3, no. 2 (April 2006): 175–78. http://dx.doi.org/10.1586/14789450.3.2.175.

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Taoufiq, Zacharie, Momchil Ninov, Alejandro Villar-Briones, Han-Ying Wang, Toshio Sasaki, Michael C. Roy, Francois Beauchain, et al. "Hidden proteome of synaptic vesicles in the mammalian brain." Proceedings of the National Academy of Sciences 117, no. 52 (December 21, 2020): 33586–96. http://dx.doi.org/10.1073/pnas.2011870117.

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Current proteomic studies clarified canonical synaptic proteins that are common to many types of synapses. However, proteins of diversified functions in a subset of synapses are largely hidden because of their low abundance or structural similarities to abundant proteins. To overcome this limitation, we have developed an “ultra-definition” (UD) subcellular proteomic workflow. Using purified synaptic vesicle (SV) fraction from rat brain, we identified 1,466 proteins, three times more than reported previously. This refined proteome includes all canonical SV proteins, as well as numerous proteins of low abundance, many of which were hitherto undetected. Comparison of UD quantifications between SV and synaptosomal fractions has enabled us to distinguish SV-resident proteins from potential SV-visitor proteins. We found 134 SV residents, of which 86 are present in an average copy number per SV of less than one, including vesicular transporters of nonubiquitous neurotransmitters in the brain. We provide a fully annotated resource of all categorized SV-resident and potential SV-visitor proteins, which can be utilized to drive novel functional studies, as we characterized here Aak1 as a regulator of synaptic transmission. Moreover, proteins in the SV fraction are associated with more than 200 distinct brain diseases. Remarkably, a majority of these proteins was found in the low-abundance proteome range, highlighting its pathological significance. Our deep SV proteome will provide a fundamental resource for a variety of future investigations on the function of synapses in health and disease.

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Gerszten, Robert E., Frank Accurso, Gordon R. Bernard, Richard M. Caprioli, Eric W. Klee, George G. Klee, Iftikhar Kullo, et al. "Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs." American Journal of Physiology-Lung Cellular and Molecular Physiology 295, no. 1 (July 2008): L16—L22. http://dx.doi.org/10.1152/ajplung.00044.2008.

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The emerging scientific field of proteomics encompasses the identification, characterization, and quantification of the protein content or proteome of whole cells, tissues, or body fluids. The potential for proteomic technologies to identify and quantify novel proteins in the plasma that can function as biomarkers of the presence or severity of clinical disease states holds great promise for clinical use. However, there are many challenges in translating plasma proteomics from bench to bedside, and relatively few plasma biomarkers have successfully transitioned from proteomic discovery to routine clinical use. Key barriers to this translation include the need for “orthogonal” biomarkers (i.e., uncorrelated with existing markers), the complexity of the proteome in biological samples, the presence of high abundance proteins such as albumin in biological samples that hinder detection of low abundance proteins, false positive associations that occur with analysis of high dimensional datasets, and the limited understanding of the effects of growth, development, and age on the normal plasma proteome. Strategies to overcome these challenges are discussed.

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Shkrigunov, Timur, Pavel Pogodin, Victor Zgoda, Olesya Larina, Yulia Kisrieva, Maria Klimenko, Oleg Latyshkevich, Peter Klimenko, Andrey Lisitsa, and Natalia Petushkova. "Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi." Current Issues in Molecular Biology 44, no. 5 (May 9, 2022): 2069–88. http://dx.doi.org/10.3390/cimb44050140.

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An important step in the proteomic analysis of missing proteins is the use of a wide range of tissues, optimal extraction, and the processing of protein material in order to ensure the highest sensitivity in downstream protein detection. This work describes a purification protocol for identifying low-abundance proteins in human chorionic villi using the proposed “1DE-gel concentration” method. This involves the removal of SDS in a short electrophoresis run in a stacking gel without protein separation. Following the in-gel digestion of the obtained holistic single protein band, we used the peptide mixture for further LC–MS/MS analysis. Statistically significant results were derived from six datasets, containing three treatments, each from two tissue sources (elective or missed abortions). The 1DE-gel concentration increased the coverage of the chorionic villus proteome. Our approach allowed the identification of 15 low-abundance proteins, of which some had not been previously detected via the mass spectrometry of trophoblasts. In the post hoc data analysis, we found a dubious or uncertain protein (PSG7) encoded on human chromosome 19 according to neXtProt. A proteomic sample preparation workflow with the 1DE-gel concentration can be used as a prospective tool for uncovering the low-abundance part of the human proteome.

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Tang, Xiaoyue, Juan Li, Wei-gang Zhao, Haidan Sun, Zhengguang Guo, Li Jing, Zhufang She, et al. "Comprehensive map and functional annotation of the mouse white adipose tissue proteome." PeerJ 7 (July 25, 2019): e7352. http://dx.doi.org/10.7717/peerj.7352.

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White adipose tissue (WAT) plays a significant role in energy metabolism and the obesity epidemic. In this study, we sought to (1) profile the mouse WAT proteome with advanced 2DLC/MS/MS approach, (2) provide insight into WAT function based on protein functional annotation, and (3) predict potentially secreted proteins. A label-free 2DLC/MS/MS proteomic approach was used to identify the WAT proteome from female mouse WAT. A total of 6,039 proteins in WAT were identified, among which 5,160 were quantified (spanning a magnitude of 106) using an intensity-based absolute quantification algorithm, and 3,117 proteins were reported by proteomics technology for the first time in WAT. To comprehensively analyze the function of WAT, the proteins were divided into three quantiles based on abundance and we found that proteins of different abundance performed different functions. High-abundance proteins (the top 90%, 1,219 proteins) were involved in energy metabolism; middle-abundance proteins (90–99%, 2,273 proteins) were involved in the regulation of protein synthesis; and low-abundance proteins (99–100%, 1,668 proteins) were associated with lipid metabolism and WAT beiging. Furthermore, 800 proteins were predicted by SignalP4.0 to have signal peptides, 265 proteins had never been reported, and five have been reported as adipokines. The above results provide a large dataset of the normal mouse WAT proteome, which might be useful for WAT function research.

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Baumann, Sven, Uta Ceglarek, Georg Martin Fiedler, Jan Lembcke, Alexander Leichtle, and Joachim Thiery. "Standardized Approach to Proteome Profiling of Human Serum Based on Magnetic Bead Separation and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry." Clinical Chemistry 51, no. 6 (June 1, 2005): 973–80. http://dx.doi.org/10.1373/clinchem.2004.047308.

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Abstract Background: Magnetic bead purification for the analysis of low-abundance proteins in body fluids facilitates the identification of potential new biomarkers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The aims of our study were to establish a proteome fractionation technique and to validate a standardized blood sampling, processing, and storage procedure for proteomic pattern analysis. Methods: We used magnetic bead separation for proteome profiling of human blood by MALDI-TOF MS (mass range, 1000–10 000 Da) and studied the effects on the quality and reproducibility of the proteome analysis of anticoagulants, blood clotting, time and temperature of sample storage, and the number of freeze–thaw cycles of samples. Results: The proteome pattern of human serum was characterized by ∼350 signals in the mass range of 1000–10 000 Da. The proteome profile showed time-dependent dynamic changes before and after centrifugation of the blood samples. Serum mass patterns differed between native samples and samples frozen once. The best reproducibility of proteomic patterns was with a single thawing of frozen serum samples. Conclusion: Application of the standardized preanalytical blood sampling and storage procedure in combination with magnetic bead-based fractionation decreases variability of proteome patterns in human serum assessed by MALDI-TOF MS.

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Fonslow, Bryan R., Paulo C. Carvalho, Katrina Academia, Steve Freeby, Tao Xu, Aleksey Nakorchevsky, Aran Paulus, and John R. Yates. "Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT." Journal of Proteome Research 10, no. 8 (August 5, 2011): 3690–700. http://dx.doi.org/10.1021/pr200304u.

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Duport, Catherine, Ludivine Rousset, Béatrice Alpha-Bazin, and Jean Armengaud. "Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature." Toxins 12, no. 10 (October 6, 2020): 645. http://dx.doi.org/10.3390/toxins12100645.

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Cellular proteomes and exoproteomes are dynamic, allowing pathogens to respond to environmental conditions to sustain growth and virulence. Bacillus cereus is an important food-borne pathogen causing intoxication via emetic toxin and/or multiple protein exotoxins. Here, we compared the dynamics of the cellular proteome and exoproteome of emetic B. cereus cells grown at low (16 °C) and high (30 °C) temperature. Tandem mass spectrometry (MS/MS)-based shotgun proteomics analysis identified 2063 cellular proteins and 900 extracellular proteins. Hierarchical clustering following principal component analysis indicated that in B. cereus the abundance of a subset of these proteins—including cold-stress responders, and exotoxins non-hemolytic enterotoxin (NHE) and hemolysin I (cereolysin O (CLO))—decreased at low temperature, and that this subset governs the dynamics of the cellular proteome. NHE, and to a lesser extent CLO, also contributed significantly to exoproteome dynamics; with decreased abundances in the low-temperature exoproteome, especially in late growth stages. Our data therefore indicate that B. cereus may reduce its production of secreted protein toxins to maintain appropriate proteome dynamics, perhaps using catabolite repression to conserve energy for growth in cold-stress conditions, at the expense of virulence.

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Deng, Ning, Zhenye Li, Chao Pan, and Huilong Duan. "freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis." Scientific World Journal 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/137076.

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Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

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Ly, Tony, Aki Endo, Alejandro Brenes, Marek Gierlinski, Vackar Afzal, Andrea Pawellek, and Angus I. Lamond. "Proteome-wide analysis of protein abundance and turnover remodelling during oncogenic transformation of human breast epithelial cells." Wellcome Open Research 3 (May 2, 2018): 51. http://dx.doi.org/10.12688/wellcomeopenres.14392.1.

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Background: Viral oncogenes and mutated proto-oncogenes are potent drivers of cancer malignancy. Downstream of the oncogenic trigger are alterations in protein properties that give rise to cellular transformation and the acquisition of malignant cellular phenotypes. Developments in mass spectrometry enable large-scale, multidimensional characterisation of proteomes. Such techniques could provide an unprecedented, unbiased view of how oncogene activation remodels a human cell proteome. Methods: Using quantitative MS-based proteomics and cellular assays, we analysed how transformation induced by activating v-Src kinase remodels the proteome and cellular phenotypes of breast epithelial (MCF10A) cells. SILAC MS was used to comprehensively characterise the MCF10A proteome and to measure v-Src-induced changes in protein abundance across seven time-points (1-72 hrs). We used pulse-SILAC MS (Boisvert et al., 2012), to compare protein synthesis and turnover in control and transformed cells. Follow-on experiments employed a combination of cellular and functional assays to characterise the roles of selected Src-responsive proteins. Results: Src-induced transformation changed the expression and/or turnover levels of ~3% of proteins, affecting ~1.5% of the total protein molecules in the cell. Transformation increased the average rate of proteome turnover and disrupted protein homeostasis. We identify distinct classes of protein kinetics in response to Src activation. We demonstrate that members of the polycomb repressive complex 1 (PRC1) are important regulators of invasion and migration in MCF10A cells. Many Src-regulated proteins are present in low abundance and some are regulated post-transcriptionally. The signature of Src-responsive proteins is highly predictive of poor patient survival across multiple cancer types. Open access to search and interactively explore all these proteomic data is provided via the EPD database (www.peptracker.com/epd). Conclusions: We present the first comprehensive analysis measuring how protein expression and protein turnover is affected by cell transformation, providing a detailed picture at the protein level of the consequences of activation of an oncogene.

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Millioni, Renato, Serena Tolin, Lucia Puricelli, Stefano Sbrignadello, Gian Paolo Fadini, Paolo Tessari, and Giorgio Arrigoni. "High Abundance Proteins Depletion vs Low Abundance Proteins Enrichment: Comparison of Methods to Reduce the Plasma Proteome Complexity." PLoS ONE 6, no. 5 (May 4, 2011): e19603. http://dx.doi.org/10.1371/journal.pone.0019603.

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Williams, Katherine E., George A. Lemieux, Maria E. Hassis, Adam B. Olshen, Susan J. Fisher, and Zena Werb. "Quantitative proteomic analyses of mammary organoids reveals distinct signatures after exposure to environmental chemicals." Proceedings of the National Academy of Sciences 113, no. 10 (February 22, 2016): E1343—E1351. http://dx.doi.org/10.1073/pnas.1600645113.

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Common environmental contaminants such as bisphenols and phthalates and persistent contaminants such as polychlorinated biphenyls are thought to influence tissue homeostasis and carcinogenesis by acting as disrupters of endocrine function. In this study we investigated the direct effects of exposure to bisphenol A (BPA), mono-n-butyl phthalate (Pht), and polychlorinated biphenyl 153 (PCB153) on the proteome of primary organotypic cultures of the mouse mammary gland. At low-nanomolar doses each of these agents induced distinct effects on the proteomes of these cultures. Although BPA treatment produced effects that were similar to those induced by estradiol, there were some notable differences, including a reduction in the abundance of retinoblastoma-associated protein and increases in the Rho GTPases Ras-related C3 botulinum toxin substrate 1 (Rac1) and cell division cycle protein CDC42. Both Pht and PCB153 induced changes that were distinct from those induced by estrogen, including decreased levels of the transcriptional corepressor C-terminal binding protein 1. Interestingly, the three chemicals appeared to alter the abundance of distinct splice forms of many proteins as well as the abundance of several proteins that regulate RNA splicing. Our combined results indicate that the three classes of chemical have distinct effects on the proteome of normal mouse mammary cultures, some estrogen-like but most estrogen independent, that influence diverse biological processes including apoptosis, cell adhesion, and proliferation.

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Weeks, Amy M., James R. Byrnes, Irene Lui, and James A. Wells. "Mapping proteolytic neo-N termini at the surface of living cells." Proceedings of the National Academy of Sciences 118, no. 8 (February 3, 2021): e2018809118. http://dx.doi.org/10.1073/pnas.2018809118.

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N terminomics is a powerful strategy for profiling proteolytic neo-N termini, but its application to cell surface proteolysis has been limited by the low relative abundance of plasma membrane proteins. Here we apply plasma membrane-targeted subtiligase variants (subtiligase-TM) to efficiently and specifically capture cell surface N termini in live cells. Using this approach, we sequenced 807 cell surface N termini and quantified changes in their abundance in response to stimuli that induce proteolytic remodeling of the cell surface proteome. To facilitate exploration of our datasets, we developed a web-accessible Atlas of Subtiligase-Captured Extracellular N Termini (ASCENT; http://wellslab.org/ascent). This technology will facilitate greater understanding of extracellular protease biology and reveal neo-N termini biomarkers and targets in disease.

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Rothwell, Stephen W., Ofer Eidelman, Catherine Jozwik, Gregory Mueller, Merrily Poth, Pamela L. Zeitlin, William Guggino, David M. Jacobowitz, Meera Srivastava, and Harvey B. Pollard. "Signalling Pathways Have Different Expression Profiles in Human Platelets Isolated from Men and Women." Blood 108, no. 11 (November 16, 2006): 1519. http://dx.doi.org/10.1182/blood.v108.11.1519.1519.

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Abstract Background: Cardiovascular diseases (CVD) are the leading causes of death for men and women in the U.S. Platelets play a central role in the inflammation and coagulation mechanisms responsible for these disorders, and anti-platelet drugs are therefore the current mainstays in prevention and therapy. Understanding the signaling pathways involved in normal and abnormal platelet function using proteomic techniques offers a novel strategic approach to the discovery of potential new therapeutic targets. Hypothesis: The incidence and outcomes of cardiovascular disease are profoundly dependent on gender, and it is possible that differences in platelet signaling mechanisms may contribute to these disparities. We have therefore hypothesized that the platelet signaling proteome is gender-specific. Methods: Platelets were isolated and purified from four normal adult male and four normal adult female donors under an IRB-approved protocol. Conventional 2D-gel electrophoresis (2DGE) and mass spectrometry were used to profile the high abundance platelet proteome. Antibody microarrays, bearing 507 monoclonal antibodies against low abundance proteins involved in signaling pathways and related functions, were used to interrogate the lower abundance platelet. Western blots were used to validate a subset of the data. Results: Discovery studies with 2DGE revealed at least nineteen lower abundance proteins which could be significantly distinguished on the basis of gender (P<0.05). Two of these proteins, a thrombopoeitin-activated G-protein component (#1101) and a megakaryocyte-relevant co-factor for DNA synthesis (#1583), were selectively elevated in male platelets. Concurrent studies on the sensitive antibody microarray platform revealed that more than 420 proteins were significantly expressed in a gender-specific manner (P<0.05). Of these, 62 remained significant by the stringent criterion of a False Discovery Rate (FDR) of <10% (SAM Algorithm, 2000 permutations). By rank-ordering the proteins by expression level, we found that platelets from normal male and female donors were significantly and uniquely enriched in different signaling proteins. These gender-specific signaling proteins included IL-1beta, and specific isoforms of iNOS (inducible nitric oxide synthase), PLC (phospholipase C), and PKC (protein kinase C). Western blot analysis validated a subset of the differentially expressed platelet proteome. Conclusions: These data support the hypothesis that the platelet signaling proteome is gender-specific. We interpret these data to indicate that gender-specific differences in the platelet signaling proteome may contribute to the gender-specific disparity in outcomes for cardiovascular diseases in men and women.

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Zoidakis, Jérôme, Ploumisti Dimitraki, Panagiotis Zerefos, and Antonia Vlahou. "Application of Preparative Electrophoresis for Clinical Proteomics in Urine: Is it Feasible?" Journal of Medical Biochemistry 28, no. 4 (October 1, 2009): 268–73. http://dx.doi.org/10.2478/v10011-009-0027-6.

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Application of Preparative Electrophoresis for Clinical Proteomics in Urine: Is it Feasible?Urine samples are easily attainable which makes them ideal substrates for biomarker research. Various techniques have been employed to unravel the urine proteome and identify disease biomarkers. Even though the presence of high abundance proteins in urine is not so pronounced as in the case of plasma, the presence of proteolytic products, many of which at low abundance, along with numerous frequently random chemical modifications, makes the analysis of urinary proteins challenging. To facilitate the detection of low abundance urinary proteins, in the study presented herein we applied two different electrophoretic techniques, preparative Lithium Dodecyl Sulfate (LDS)-PAGE in combination with 2-DE for urinary protein separation and enrichment. Our results indicate the effectiveness of this approach for the enrichment of low abundance and low molecular weight proteins and peptides in urine, and contribute towards the establishment of a urinary proteomic database. The application of this technique as a biomarker discovery tool faces several challenges: these include down-scaling of the technique, possible recompensation for the consequent expected decrease in protein resolution, by optimizing steps of the experimental workflow as well as getting a good understanding of the technical variability of the technique. Under these conditions, preparative electrophoresis can become an effective tool for clinical proteomics applications.

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Jung, Ju-Young, Cheol Woo Min, So Wun Kim, Ravi Gupta, Woojong Jang, Kyong-Hwan Bang, Yu-Jin Kim, Ick-Hyun Jo, and Sun Tae Kim. "Proteomic Analysis of Ginseng (Panax ginseng C. A. Meyer) Fluid Proteins under Salt Stress." Agronomy 12, no. 9 (August 28, 2022): 2048. http://dx.doi.org/10.3390/agronomy12092048.

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Ginseng (Panax ginseng C. A. Meyer), due to its relatively longer cultivation time, is often exposed to environmental stresses such as heat, salt, and drought. Particularly, salt-stress-derived oxidative damages greatly affect photosynthetic efficiency and consequently cause reduction of growth, development, and yield of ginseng. Thus, efforts have been made to understand the salt-stress-induced changes at proteome levels; however, the overall understanding of possible salt-responsive proteins in ginseng is still limited because of their low-abundance. A growing body of evidence suggests that plants secrete various low-abundant proteins localized in the intra- and extracellular spaces during stress conditions, and those proteins may have a key role for salt tolerance. Therefore, here, we report the ginseng fluids proteome to identify the potential salt-responsive proteins. This approach led to the identification of 261 secreted fluid proteins, and functional categorization revealed that identified proteins were majorly associated with photosynthesis, protein synthesis, cell binding, and various metabolisms. Further validation using qRT-PCR analysis showed similar expression profiles of heat-shock protein 70, glycosyl hydrolase 17, and fructose-bisphosphate aldolase class-I with proteome results. Overall, ginseng fluid proteomic analysis successfully identified the potential salt-responsive proteins, which might be helpful for understanding of salt-tolerance mechanisms in ginseng.

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Gygi, Steven P., Beate Rist, Timothy J. Griffin, Jimmy Eng, and Ruedi Aebersold. "Proteome Analysis of Low-Abundance Proteins Using Multidimensional Chromatography and Isotope-Coded Affinity Tags." Journal of Proteome Research 1, no. 1 (February 2002): 47–54. http://dx.doi.org/10.1021/pr015509n.

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Saand, Mumtaz Ali, Jing Li, Yi Wu, Lixia Zhou, Hongxing Cao, and Yaodong Yang. "Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress." International Journal of Molecular Sciences 23, no. 23 (November 29, 2022): 14926. http://dx.doi.org/10.3390/ijms232314926.

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Oil palm (Elaeis guineensis Jacq.) is an economically important tropical oil crop widely cultivated in tropical zones worldwide. Being a tropical crop, low-temperature stress adversely affects the oil palm. However, integrative leaf transcriptomic and proteomic analyses have not yet been conducted on an oil palm crop under cold stress. In this study, integrative omics transcriptomic and iTRAQ-based proteomic approaches were employed for three oil palm varieties, i.e., B × E (Bamenda × Ekona), O × G (E. oleifera × Elaeis guineensis), and T × E (Tanzania × Ekona), in response to low-temperature stress. In response to low-temperature stress at (8 °C) for 5 days, a total of 5175 up- and 2941 downregulated DEGs in BE-0_VS_BE-5, and a total of 3468 up- and 2443 downregulated DEGs for OG-0_VS_OG-5, and 3667 up- and 2151 downregulated DEGs for TE-0_VS_TE-5 were identified. iTRAQ-based proteomic analysis showed 349 up- and 657 downregulated DEPs for BE-0_VS_BE-5, 372 up- and 264 downregulated DEPs for OG-0_VS_OG-5, and 500 up- and 321 downregulated DEPs for TE-0_VS_TE-5 compared to control samples treated at 28 °C and 8 °C, respectively. The KEGG pathway correlation of oil palm has shown that the metabolic synthesis and biosynthesis of secondary metabolites pathways were significantly enriched in the transcriptome and proteome of the oil palm varieties. The correlation expression pattern revealed that TE-0_VS_TE-5 is highly expressed and BE-0_VS_BE-5 is suppressed in both the transcriptome and proteome in response to low temperature. Furthermore, numerous transcription factors (TFs) were found that may regulate cold acclimation in three oil palm varieties at low temperatures. Moreover, this study identified proteins involved in stresses (abiotic, biotic, oxidative, and heat shock), photosynthesis, and respiration in iTRAQ-based proteomic analysis of three oil palm varieties. The increased abundance of stress-responsive proteins and decreased abundance of photosynthesis-related proteins suggest that the TE variety may become cold-resistant in response to low-temperature stress. This study may provide a basis for understanding the molecular mechanism for the adaptation of oil palm varieties in response to low-temperature stress in China.

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Min, Cheol Woo, Joonho Park, Jin Woo Bae, Ganesh Kumar Agrawal, Randeep Rakwal, Youngsoo Kim, Pingfang Yang, Sun Tae Kim, and Ravi Gupta. "In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis." Cells 9, no. 6 (June 22, 2020): 1517. http://dx.doi.org/10.3390/cells9061517.

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Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.

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Gegenfurtner, Katrin, Thomas Fröhlich, Florian Flenkenthaler, Miwako Kösters, Sébastien Fritz, Olivier Desnoës, Daniel Le Bourhis, et al. "Genetic merit for fertility alters the bovine uterine luminal fluid proteome†." Biology of Reproduction 102, no. 3 (November 30, 2019): 730–39. http://dx.doi.org/10.1093/biolre/ioz216.

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Abstract Over the last decades, fertility of dairy cows has declined due to selection strategies focusing on milk yield. To study the effect of genetic merit for fertility on the proteome of the bovine uterine luminal fluid, Holstein heifers with low- and two groups of heifers with high-fertility index (high-fertility Holstein and Montbéliarde) were investigated. To focus on the maternal effect, heifers from all groups were synchronized and received on Day 7 high-quality embryos. Uterine luminal fluid from Day 19 pregnant heifers was analyzed in a holistic proteomic approach using nano-LC-MS/MS analysis combined with a label-free quantification approach. In total, 1737 proteins were identified, of which 597 differed significantly in abundance between the three groups. The vast majority of proteome differences was found comparing both high-fertility groups to the low-fertility Holstein group, showing that the genetic predisposition for fertility is prevalent regarding the uterine luminal fluid proteome. Evaluation of this dataset using bioinformatic tools revealed an assignment of higher abundant proteins in low-fertility Holstein to several metabolic processes, such as vitamin metabolic process, which comprises folate receptor alpha (FOLR1) and retinol-binding protein, indicating an involvement of disturbed metabolic processes in decreased fertility. Moreover, immune system-related proteins — lactotransferrin and chromogranin A — were enriched in low-fertility cows together with interferon tau 3 h and interferon tau-2. Our results indicate that the genetic merit for fertility leads to substantial quantitative differences at the level of proteins in uterine fluid of pregnant animals, thus altering the microenvironment for the early conceptus.

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Boschetti, Egisto, and Pier Giorgio Righetti. "Hexapeptide combinatorial ligand libraries: the march for the detection of the low-abundance proteome continues." BioTechniques 44, no. 5 (April 2008): 663–65. http://dx.doi.org/10.2144/000112762.

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Righetti, Pier Giorgio, and Egisto Boschetti. "Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications." Plant Science 290 (January 2020): 110302. http://dx.doi.org/10.1016/j.plantsci.2019.110302.

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Bargiela, Rafael, Karin Lanthaler, Colin M. Potter, Manuel Ferrer, Alexander F. Yakunin, Bela Paizs, Peter N. Golyshin, and Olga V. Golyshina. "Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum." Microorganisms 8, no. 5 (May 19, 2020): 759. http://dx.doi.org/10.3390/microorganisms8050759.

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The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. The highest increase in expression appeared in low-abundance (0.001–0.005 fmol%) proteins for polypeptides’ hydrolysis (metal-dependent hydrolase), oxidation of amino acids (FAD-dependent oxidoreductase), pyrimidine biosynthesis (aspartate carbamoyltransferase regulatory chain proteins), citrate cycle (2-oxoacid ferredoxin oxidoreductase) and ATP production (V type ATP synthase). Importantly, the cold shock induced a substantial increase (6% and 9%) in expression of the most-abundant proteins, thermosome beta subunit and glutamate dehydrogenase. This study has outlined potential mechanisms of environmental fitness of Cuniculiplasma spp. allowing them to colonise acidic settings at low/moderate temperatures.

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Dasari, Surendra, Sean A. Newsom, Sarah E. Ehrlicher, Harrison D. Stierwalt, and Matthew M. Robinson. "Remodeling of skeletal muscle mitochondrial proteome with high-fat diet involves greater changes to β-oxidation than electron transfer proteins in mice." American Journal of Physiology-Endocrinology and Metabolism 315, no. 4 (October 1, 2018): E425—E434. http://dx.doi.org/10.1152/ajpendo.00051.2018.

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Excess fat intake can increase lipid oxidation and expression of mitochondrial proteins, indicating remodeling of the mitochondrial proteome. Yet intermediates of lipid oxidation also accumulate, indicating a relative insufficiency to completely oxidize lipids. We investigated remodeling of the mitochondrial proteome to determine mechanisms of changes in lipid oxidation following high-fat feeding. C57BL/6J mice consumed a high-fat diet (HFD, 60% fat from lard) or a low-fat diet (LFD, 10% fat) for 12 wk. Mice were fasted for 4 h and then anesthetized by pentobarbital sodium overdose for tissue collection. A mitochondrial-enriched fraction was prepared from gastrocnemius muscles and underwent proteomic analysis by high-resolution mass spectrometry. Mitochondrial respiratory efficiency was measured as the ratio of ATP production to O2 consumption. Intramuscular acylcarnitines were measured by liquid chromatography-mass spectrometry. A total of 658 mitochondrial proteins were identified: 40 had higher abundance and 14 had lower abundance in mice consuming the HFD than in mice consuming the LFD. Individual proteins that changed with the HFD were primarily related to β-oxidation; there were fewer changes to the electron transfer system. Gene set enrichment analysis indicated that the HFD increased pathways of lipid metabolism and β-oxidation. Intramuscular concentrations of select acylcarnitines (C18:0) were greater in the HFD mice and reflected dietary lipid composition. Mitochondrial respiratory ATP production-to-O2 consumption ratio for lipids was not different between LFD and HFD mice. After the 60% fat diet, remodeling of the mitochondrial proteome revealed upregulation of proteins regulating lipid oxidation that was not evident for all mitochondrial pathways. The accumulation of lipid metabolites with obesity may occur without intrinsic dysfunction to mitochondrial lipid oxidation.

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Signer, Robert. "Proteostasis and Myeloid Stem Cell Production." Blood 134, Supplement_1 (November 13, 2019): SCI—42—SCI—42. http://dx.doi.org/10.1182/blood-2019-121085.

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Hematopoietic stem cells (HSCs) regenerate blood cells lost to turnover, injury and disease. Defects in HSC maintenance, such as those that occur during aging, lead to anemia, impaired immunity, and bone marrow failure. Over- or ectopic activation of HSC self-renewal programs leads to hematopoietic neoplasms. Thus, defects in HSC maintenance can lead to diverse malignant and non-malignant hematopoietic disorders. We recently discovered that HSCs have lower rates of protein synthesis than other blood cells. Low protein synthesis is necessary for HSCs, as genetic changes that increase protein synthesis impair HSC function. Importantly, this does not simply reflect HSC quiescence, as dividing HSCs also have lower rates of protein synthesis as compared to dividing restricted progenitors. However, why stem cells depend on low protein synthesis and how increases in protein synthesis impair stem cell function remain largely unknown. Translation is a key cog in both the gene expression and protein homeostasis (proteostasis) networks, and thus influences both the content and the quality of the proteome. We have now determined that low protein synthesis within HSCs is associated with elevated proteome quality in vivo. HSCs contain less ubiquitylated and unfolded proteins as compared to restricted myeloid progenitors, and modest increases in protein synthesis cause an accumulation of misfolded/unfolded proteins within HSCs. Thus, HSCs depend upon low protein synthesis to maintain proteome quality. To test how translational control of proteome quality affects stem cell function, we examined Aarssti/sti mice that harbor a mutation in the alanyl-tRNA synthetase, which causes a tRNA editing defect that increases amino acid misincorporation errors during translation. Aarssti/sti mice exhibit reduced HSC numbers and significantly diminished serial reconstituting activity in vivo, but do not exhibit defects within restricted progenitors. Surprisingly, a modest accumulation of misfolded/unfolded proteins does not induce significant activation of the unfolded protein response within HSCs, but instead overwhelms the capacity of the proteasome, which promotes the stabilization and increased abundance of c-Myc. Conditional deletion of a single copy of Myc is sufficient to significantly rescue serial reconstitution defects in Aarssti/sti HSCs. HSCs are thus dependent on low protein synthesis to maintain proteome quality and homeostasis to preserve their self-renewal activity in vivo. Disclosures No relevant conflicts of interest to declare.

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Askeland, Anders, Anne Borup, Ole Østergaard, Jesper V. Olsen, Sigrid M. Lund, Gunna Christiansen, Søren R. Kristensen, Niels H. H. Heegaard, and Shona Pedersen. "Mass-Spectrometry Based Proteome Comparison of Extracellular Vesicle Isolation Methods: Comparison of ME-kit, Size-Exclusion Chromatography, and High-Speed Centrifugation." Biomedicines 8, no. 8 (July 25, 2020): 246. http://dx.doi.org/10.3390/biomedicines8080246.

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Extracellular vesicles (EVs) are small membrane-enclosed particles released by cells under various conditions specific to cells’ biological states. Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. MS analysis of EVs in plasma is challenging and EV isolation is usually necessary. Therefore, we compared differences in abundance, subtypes, and contamination for EVs isolated by high-speed centrifugation, size exclusion chromatography (SEC), and peptide-affinity precipitation (PAP/ME kit) for subsequent MS-based proteome analysis. Successful EV isolation was evaluated by nanoparticle-tracking analysis, immunoblotting, and transmission electron microscopy, while EV abundance, EV subtypes, and contamination was evaluated by label-free tandem MS. High-speed centrifugation and SEC isolates showed high EV abundance at the expense of contamination by non-EV proteins and lipoproteins, respectively. These two methods also resulted in EVs of a similar type, however, with smaller EVs in SEC isolates. PAP isolates had a relatively low EV abundance and high contamination. We consider high-speed centrifugation and SEC suitable as EV isolation for MS biomarker studies, where the choice between the two should depend on the scientific questions and whether the focus is on larger or smaller EVs or a combination of both.

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El Rabey, Haddad A., Abdulrahman L. Al-Malki, and Khalid O. Abulnaja. "Proteome Analysis of Date Palm (Phoenix dactylifera L.) under Severe Drought and Salt Stress." International Journal of Genomics 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/7840759.

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Date palm cultivars differently tolerate salinity and drought stress. This study was carried out to study the response of date palm to severe salinity and drought based on leaf proteome analysis. Eighteen-month-old date palm plants were subjected to severe salt (48 g/L NaCl) and drought (82.5 g/L PEG or no irrigation) conditions for one month. Using a protein 2D electrophoresis method, 55 protein spots were analyzed using mass spectrometry. ATP synthase CF1 alpha chains were significantly upregulated under all three stress conditions. Changes in the abundance of RubisCO activase and one of the RubisCO fragments were significant in the same spots only for salt stress and drought stress with no irrigation, and oxygen-evolving enhancer protein 2 was changed in different spots. Transketolase was significantly changed only in drought stress with PEG. The expression of salt and drought stress genes of the chosen protein spots was either overexpressed or downexpressed as revealed by the high or low protein abundance, respectively. In addition, all drought tolerance genes due to no irrigation were downregulated. In conclusion, the proteome analysis of date palm under salinity and drought conditions indicated that both salinity and drought tolerance genes were differentially expressed resulting in high or low protein abundance of the chosen protein spots as a result of exposure to drought and salinity stress condition.

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Righetti, Pier, Egisto Boschetti, and Bernard Monsarrat. "The “Invisible Proteome”: How to Capture the Low-Abundance Proteins Via Combinatorial Ligand Libraries." Current Proteomics 4, no. 4 (December 1, 2007): 198–208. http://dx.doi.org/10.2174/157016407783221277.

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Hernández-Castellano, Lorenzo, André Almeida, Miguel Ventosa, Ana Coelho, Noemí Castro, and Anastasio Argüello. "The effect of colostrum intake on blood plasma proteome profile in newborn lambs: low abundance proteins." BMC Veterinary Research 10, no. 1 (2014): 85. http://dx.doi.org/10.1186/1746-6148-10-85.

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Pedersen, Susanne K., Jenny L. Harry, Lucille Sebastian, Jasmine Baker, Mathew D. Traini, John T. McCarthy, Abi Manoharan, et al. "Unseen Proteome: Mining Below the Tip of the Iceberg To Find Low Abundance and Membrane Proteins." Journal of Proteome Research 2, no. 3 (June 2003): 303–11. http://dx.doi.org/10.1021/pr025588i.

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Lu, Chih-Ming, Yu-Jen Wu, Cheng-Chi Chen, Jue-Liang Hsu, Jiing-Chuan Chen, Jeff Chen, Chun-Hsiung Huang, and Ying-Chin Ko. "Identification of low-abundance proteins via fractionation of the urine proteome with weak anion exchange chromatography." Proteome Science 9, no. 1 (2011): 17. http://dx.doi.org/10.1186/1477-5956-9-17.

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Bantscheff, Marcus. "Egisto Boschetti and Pier Giorgio Righetti: Low-abundance proteome discovery: state of the art and protocols." Analytical and Bioanalytical Chemistry 406, no. 9-10 (February 18, 2014): 2221–22. http://dx.doi.org/10.1007/s00216-014-7645-7.

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Kim, Hyunju, Kerry Shulze, Casey Rebholz, Gwen Sincerbeaux, Lee Shu-Fane Wu, Sarah Baker, James Yager, et al. "Constructing a Plasma Nutriproteome for Population Assessment: Analytical Considerations." Current Developments in Nutrition 6, Supplement_1 (June 2022): 770. http://dx.doi.org/10.1093/cdn/nzac063.012.

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Abstract Objectives Micronutrient status is rarely assessed in low-income settings. Proteomics may offer a proxy by measuring plasma proteins correlated with nutrients on a single platform. However, the proteome is huge, diverse and measured in different ways. We describe an analytic framework and decision process to explore nutrient: protein (N:P) associations for micronutrient status assessment. Methods In plasma of 435 1st trimester women in rural Bangladesh, we compared relative protein abundance, revealed by a multiplexed slow off-rate modified aptamer assay (SomaLogic, Inc), to biochemical concentrations of vitamins A, D, E, B9, B12, Zn, Se, Cu, I, & Fe, 5 carotenoids, cholesterol and AGP. After log2-transforming protein abundance per convention, N:P relationships were summarized by simple linear regression. We assessed reliability by Pearson correlation (rp) and coefficients of variation (CV) in 20 blind duplicates. To define each plasma nutriproteome [proteins correlating at a false discovery rate < 0.05], in all samples we explored a) normalizing protein abundance to the median of our sample vs not, b) assessing correlations by rp vs Spearman rank (rs) estimators, and c) log2-transforming (log2) nutrients vs not. We compared differences in the number of proteins and N:P correlative strength (either more negative/positive by rp or rs) in each proteome when nutrient concentrations were left untransformed vs log2-transformed. Results In duplicates, log2-transformed proteins that were normalized, vs not, to the sample-specific median generated higher median rp (0.92 vs. 0.87) and rs (0.87 vs. 0.85) and lower CV (4.8% vs. 11.7%). The median (IQR) size of the nutriproteomes was 147 (41–340) proteins by rp and 87 (29–639) by rs. For >50% of proteins in 13 nutriproteomes, rp was stronger than rs (in either +/− direction), favoring use of rp. Log2-transforming folate (B9), Zn & cholesterol increased proteome size by 39, 223 & 875 proteins and strengthened rp for >50% of proteins than untransformed nutrients. Other proteomes remained larger when nutrient concentrations remained untransformed. Conclusions Comparing plasma protein: nutrient associations via methods of normalization, transformation, and correlation offers a framework to guide plasma nutriproteome definition. Funding Sources Johns Hopkins University.

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Bhawal, Ruchika, Ann L. Oberg, Sheng Zhang, and Manish Kohli. "Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer." Cancers 12, no. 9 (August 27, 2020): 2428. http://dx.doi.org/10.3390/cancers12092428.

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Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.

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Helena Duarte Sagawa, Cíntia, Paulo A. Zaini, Renata de A. B. Assis, Houston Saxe, Michelle Salemi, Aaron Jacobson, Phillip A. Wilmarth, Brett S. Phinney, and Abhaya M. Dandekar. "Deep Learning Neural Network Prediction Method Improves Proteome Profiling of Vascular Sap of Grapevines during Pierce’s Disease Development." Biology 9, no. 9 (September 1, 2020): 261. http://dx.doi.org/10.3390/biology9090261.

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Plant secretome studies highlight the importance of vascular plant defense proteins against pathogens. Studies on Pierce’s disease of grapevines caused by the xylem-limited bacterium Xylella fastidiosa (Xf) have detected proteins and pathways associated with its pathobiology. Despite the biological importance of the secreted proteins in the extracellular space to plant survival and development, proteome studies are scarce due to methodological challenges. Prosit, a deep learning neural network prediction method is a powerful tool for improving proteome profiling by data-independent acquisition (DIA). We explored the potential of Prosit’s in silico spectral library predictions to improve DIA proteomic analysis of vascular leaf sap from grapevines with Pierce’s disease. The combination of DIA and Prosit-predicted libraries increased the total number of identified grapevine proteins from 145 to 360 and Xf proteins from 18 to 90 compared to gas-phase fractionation (GPF) libraries. The new proteins increased the range of molecular weights, assisted in the identification of more exclusive peptides per protein, and increased identification of low-abundance proteins. These improvements allowed identification of new functional pathways associated with cellular responses to oxidative stress, to be investigated further.

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Wang, Qi, Zhouxian Li, Jiahua Zhou, Yan Wang, Keyun Wang, Hongqiang Qin, and Mingliang Ye. "Chemical Depletion of Histidine-Containing Peptides Allows Identification of More Low-Abundance Methylation Sites from Proteome Samples." Journal of Proteome Research 20, no. 5 (March 8, 2021): 2497–505. http://dx.doi.org/10.1021/acs.jproteome.0c00976.

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Freeby, S., K. Academia, T. Wehr, N. Liu, and A. Paulus. "Enrichment of Interleukins and Low Abundance Proteins from Tissue Leakage in Serum Proteome Studies Using ProteoMiner Beads." Journal of Proteomics & Bioinformatics S2, no. 01 (July 2008): 171. http://dx.doi.org/10.4172/jpb.s1000127.

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Merali, Salim, Carlos A. Barrero, Russell P. Bowler, Diane Er Chen, Gerard Criner, Alan Braverman, Samuel Litwin, Anthony Yeung, and Steven G. Kelsen. "Analysis of the Plasma Proteome in COPD: Novel Low Abundance Proteins Reflect the Severity of Lung Remodeling." COPD: Journal of Chronic Obstructive Pulmonary Disease 11, no. 2 (October 10, 2013): 177–89. http://dx.doi.org/10.3109/15412555.2013.831063.

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Kasthuri, Raj S., Lorraine B. Anderson, LeeAnn Higgins, Jorge Di Paola, Georges E. Rivard, Catherine P. M. Hayward, and Nigel S. Key. "Proteomics in the Study of Qualitative Platelet Defects: Validation of the Approach in the Gray Platelet Syndrome and Quebec Platelet Disorder." Blood 110, no. 11 (November 16, 2007): 3900. http://dx.doi.org/10.1182/blood.v110.11.3900.3900.

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Abstract Qualitative platelet defects are a heterogeneous group of disorders characterized by abnormal platelet function. Currently available laboratory assays lack sensitivity and specificity for detecting Storage Pool and Platelet Secretion defects. The Gray Platelet Syndrome (GPS) is an autosomal recessive disorder characterized by a decrease or absence of alpha granule contents. The Quebec Platelet Disorder (QPD) results from proteolysis of alpha granule proteins due to increased amounts of platelet urokinase. A decrease or deficiency of multimerin is characteristic. Proteomics is a rapidly developing field with great promise in the study of pathophysiology and biomarker development. Recent advances have made measurement of relative protein abundance in multiple samples feasible. We used one such approach, “isotope Tagging for Relative and Absolute Quantitation” (iTRAQ) to characterize the platelet proteome of healthy volunteers and patients with GPS and QPD. iTRAQ allows analysis of up to 4 different samples simultaneously, and differences in protein abundance as low as 20% are reliably detected. The platelet proteomes of 4 healthy volunteers were analyzed. Platelet proteome analysis of study patients was as follows; 2 GPS patients compared to 2 controls; 2 heterozygous GPS patients compared to a homozygote and a control; and 3 QPD patients compared to a control. For comparison, platelet proteins were grouped by location into 3 groups - receptor, alpha granule and cytoskeletal proteins. The results are shown in the figure. Protein abundance in healthy volunteers was very consistent, with inter-individual variability ≤ 20%. Distribution of receptor and cytoskeletal proteins in GPS patients mirrored the controls, but alpha granule proteins were significantly decreased as expected. Comparison of homozygous to heterozygous GPS platelets showed this to be true only in the homozygotes, again, as expected (figure inset). Variable decreases in alpha granule proteins were observed in QPD patients but this was less profound. Multimerin was detected in QPD patients, but at levels significantly lower than controls. While urokinase was not detected in QPD platelets in this study, it was detected in a parallel study evaluating platelet releasates. The iTRAQ technique was reproducible and yielded consistent results, but currently is a relatively expensive and time-consuming approach. In summary, our results suggest that the platelet proteome is tightly regulated and very stable in healthy individuals. A significant decrease in alpha granule proteins was noted in patients with GPS but this was less remarkable in the QPD group, probably because peptides resulting from urokinase-mediated proteolysis are still labeled and quantified. Figure Figure

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Gao, Mingxia, Chunhui Deng, Wenjia Yu, Yang Zhang, Pengyuan Yang, and Xiangmin Zhang. "Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatography." PROTEOMICS 8, no. 5 (March 2008): 939–47. http://dx.doi.org/10.1002/pmic.200600099.

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Lillis, Peter E., Christine T. Griffin, and James C. Carolan. "The effect of temperature conditioning (9°C and 20°C) on the proteome of entomopathogenic nematode infective juveniles." PLOS ONE 17, no. 4 (April 7, 2022): e0266164. http://dx.doi.org/10.1371/journal.pone.0266164.

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Entomopathogenic nematodes (EPN) of the genera Steinernema and Heterorhabditis are parasites which kill and reproduce within insects. While both have life cycles centred around their developmentally arrested, nonfeeding and stress tolerant infective juvenile (IJ) stage, they are relatively distantly related. These IJs are promising biocontrol agents, and their shelf life and stress tolerance may be enhanced by storage at low temperatures. The purpose of this study was to investigate how the proteome of the IJs of two distantly related EPN species is affected by storage at 9°C (for up to 9 weeks) and 20°C (for up to 6 weeks), using label-free quantitative proteomics. Overall, more proteins were detected in S. carpocapsae (2422) than in H. megidis (1582). The S. carpocapsae proteome was strongly affected by temperature, while the H. megidis proteome was affected by both time and temperature. The proteins which increased in abundance to the greatest extent in S. carpocapsae IJs after conditioning at 9°C were chaperone proteins, and proteins related to stress. The proteins which increased in abundance the most after storage at 20°C were proteins related to the cytoskeleton, cell signalling, proteases and their inhibitors, which may have roles in infection. The proteins which decreased in abundance to the greatest extent in S. carpocapsae after both 9°C and 20°C storage were those associated with metabolism, stress and the cytoskeleton. After storage at both temperatures, the proteins increased to the greatest extent in H. megidis IJs were those associated with the cytoskeleton, cell signalling and carbon metabolism, and the proteins decreased in abundance to the greatest extent were heat shock and ribosomal proteins, and those associated with metabolism. As the longest-lived stage of the EPN life cycle, IJs may be affected by proteostatic stress, caused by the accumulation of misfolded proteins and toxic aggregates. The substantial increase of chaperone proteins in S. carpocapsae, and to a greater extent at 9°C, and the general decrease in ribosomal and chaperone proteins in H. megidis may represent species-specific proteostasis mechanisms. Similarly, organisms accumulate reactive oxygen species (ROS) over time and both species exhibited a gradual increase in proteins which enhance ROS tolerance, such as catalase. The species-specific responses of the proteome in response to storage temperature, and over time, may reflect the phylogenetic distance and/or different ecological strategies.

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Scuderi, Richard A., David B. Ebenstein, Ying-Wai Lam, Jana Kraft, and Sabrina L. Greenwood. "Inclusion of grape marc in dairy cattle rations alters the bovine milk proteome." Journal of Dairy Research 86, no. 2 (May 2019): 154–61. http://dx.doi.org/10.1017/s0022029919000372.

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AbstractGrape marc (GPM) is a viticulture by-product that is rich in secondary compounds, including condensed tannins (CT), and is used as a supplement in livestock feeding practices. The aim of this study was to determine whether feeding GPM to lactating dairy cows would alter the milk proteome through changes in nitrogen (N) partitioning. Ten lactating Holstein cows were fed a total mixed ration (TMR) top-dressed with either 1.5 kg dry matter (DM)/cow/day GPM (GPM group; n = 5) or 2.0 kg DM/cow/day of a 50:50 beet pulp: soy hulls mix (control group; n = 5). Characterization of N partitioning and calculation of N partitioning was completed through analysis of plasma urea-N, urine, feces, and milk urea-N. Milk samples were collected for general composition analysis, HPLC quantification of the high abundance milk proteins (including casein isoforms, α-lactalbumin, and β-lactoglobulin) and liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the low abundance protein enriched milk fraction. No differences in DMI, N parameters, or calculated N partitioning were observed across treatments. Dietary treatment did not affect milk yield, milk protein or fat content or yield, or the concentrations of high abundance milk proteins quantified by HPLC analysis. Of the 127 milk proteins that were identified by LC-MS/MS analysis, 16 were affected by treatment, including plasma proteins and proteins associated with the blood-milk barrier, suggesting changes in mammary passage. Immunomodulatory proteins, including butyrophilin subfamily 1 member 1A and serum amyloid A protein, were higher in milk from GPM-fed cows. Heightened abundance of bioactive proteins in milk caused by dietary-induced shifts in mammary passage could be a feasible method to enhance the healthfulness of milk for both the milk-fed calf and human consumer. Additionally, the proteome shifts observed in this trial could provide a starting point for the identification of biomarkers suitable for use as indicators of mammary function.

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Riding, G. A., S. A. Lehnert, A. J. French, and J. R. Hill. "264. Proteomic approaches to the study of conceptus fluids from first trimester bovine pregnancies." Reproduction, Fertility and Development 17, no. 9 (2005): 108. http://dx.doi.org/10.1071/srb05abs264.

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Advanced reproductive technologies using in vitro production systems in cattle and other livestock species offer significant opportunities for improving the reproductive performance of the female. Impeding the development is the overall inefficiency and significant costs surrounding the high incidence of embryo wastage, particularly during early pregnancy and the occurrence of foetal developmental abnormalities, placentation irregularities and late term losses. Effective molecular interchange and communication between the conceptus and its mother is of utmost importance for the development, growth and continued viability of the foetus. We are using a proteomics approach to determine the protein profile (proteome) of the conceptus fluids (amniotic and allantoic) during the first trimester of normal, IVF and NT pregnancies. Proteomic analysis and comparison of the proteins present in these fluids may lead to the discovery of novel biomarkers which can be used to determine foetal viability status. Collections of foetal fluids from abattoir collections of Day 35 to Day 100 pregnancies were characterised with respect to volume and total protein estimates and subjected to various fractionation procedures. Protein fingerprints of conceptus fluid fractions have been generated by two-dimensional electrophoresis and the identity of proteins determined by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry and database searches. Enrichment of the low-abundance and low molecular weight proteins has been achieved by ultrafiltration under denaturing and reducing conditions. We were able to establish the identity of the majority of high-abundance proteins and a significant proportion of low-abundance proteins in both amniotic and allantoic fluids using this method. Searching of MSDB or NCBInr mammalian protein sequence databases coupled with the putative protein database deduced from the first draft assembly of the bovine genome sequence, was achieved using Mascot software.

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Ramakrishnan, Reshmi, Bert Houben, Frederic Rousseau, and Joost Schymkowitz. "Differential proteostatic regulation of insoluble and abundant proteins." Bioinformatics 35, no. 20 (March 23, 2019): 4098–107. http://dx.doi.org/10.1093/bioinformatics/btz214.

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Abstract Motivation Despite intense effort, it has been difficult to explain chaperone dependencies of proteins from sequence or structural properties. Results We constructed a database collecting all publicly available data of experimental chaperone interaction and dependency data for the Escherichia coli proteome, and enriched it with an extensive set of protein-specific as well as cell-context-dependent proteostatic parameters. Employing this new resource, we performed a comprehensive meta-analysis of the key determinants of chaperone interaction. Our study confirms that GroEL client proteins are biased toward insoluble proteins of low abundance, but for client proteins of the Trigger Factor/DnaK axis, we instead find that cellular parameters such as high protein abundance, translational efficiency and mRNA turnover are key determinants. We experimentally confirmed the finding that chaperone dependence is a function of translation rate and not protein-intrinsic parameters by tuning chaperone dependence of Green Fluorescent Protein (GFP) in E.coli by synonymous mutations only. The juxtaposition of both protein-intrinsic and cell-contextual chaperone triage mechanisms explains how the E.coli proteome achieves combining reliable production of abundant and conserved proteins, while also enabling the evolution of diverging metabolic functions. Availability and implementation The database will be made available via http://phdb.switchlab.org. Supplementary information Supplementary data are available at Bioinformatics online.

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Ernoult, Emilie, Anthony Bourreau, Erick Gamelin, and Catherine Guette. "A Proteomic Approach for Plasma Biomarker Discovery with iTRAQ Labelling and OFFGEL Fractionation." Journal of Biomedicine and Biotechnology 2010 (2010): 1–8. http://dx.doi.org/10.1155/2010/927917.

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Human blood plasma contains a plethora of proteins, encompassing not only proteins that have plasma-based functionalities, but also possibly every other form of low concentrated human proteins. As it circulates through the tissues, the plasma picks up proteins that are released from their origin due to physiological events such as tissue remodeling and cell death. Specific disease processes or tumors are often characterized by plasma “signatures,” which may become obvious via changes in the plasma proteome profile, for example, through over expression of proteins. However, the wide dynamic range of proteins present in plasma makes their analysis very challenging, because high-abundance proteins tend to mask those of lower abundance. In the present study, we used a strategy combining iTRAQ as a reagent which improved the peptide ionization and peptide OFFGEL fractionation that has already been shown, in our previous research, to improve the proteome coverage of cellular extracts. Two prefractioning methods were compared: immunodepletion and a bead-based library of combinatorial hexapeptide technology. Our data suggested that both methods were complementary, with regard to the number of identified proteins. iTRAQ labelling, in association with OFFGEL fractionation, allowed more than 300 different proteins to be characterized from 400 μg of plasma proteins.

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Wilmes, Boris, Holger Kock, Susanne Glagla, Dirk Albrecht, Birgit Voigt, Stephanie Markert, Antje Gardebrecht, et al. "Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic BacteriumPseudoalteromonas haloplanktisTAC125." Applied and Environmental Microbiology 77, no. 4 (December 23, 2010): 1276–83. http://dx.doi.org/10.1128/aem.01750-10.

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ABSTRACTThe psychrophilic model bacteriumPseudoalteromonas haloplanktisis characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, ofP. haloplanktisstrain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacteriumP. haloplanktisin its natural environments.

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Pier Giorgio, Righetti, and Boschetti Egisto. "Pillaging plucking plundering ransacking proteomes via CPLL technology." Open Journal of Proteomics and Genomics 8, no. 1 (February 8, 2023): 001–10. http://dx.doi.org/10.17352/ojpg.000012.

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No proteome can be considered “democratic”, but rather “oligarchic” since a few proteins dominate the landscape and often obliterate the signal of the rare ones. That is the reason why most scientists lament that, in proteome analysis, the same set of abundant proteins is repeatedly seen. Current pre-fractionation techniques, one way or another, are besieged by problems, in that they are based on a “depletion principle”, i.e. elimination of unwanted species. Yet “democracy” calls for giving “equal rights” to everyone. One way to achieve that would be the use of libraries of combinatorial ligands coupled to spherical beads. When these beads are contacted with complex proteomes (e.g., human urines and sera, egg white, any cell or tissue lysate) of widely differing protein composition and relative abundances, they are able to “normalize” the protein population, by sharply reducing the concentration of the most abundant components while simultaneously enhancing the level of the most dilute components. It is felt that this method could offer a strong step forward in bringing the “unseen proteome” (due to either low abundance and/or presence of interferences) within the detection capabilities of current proteomics detection methods. Examples are given of the normalization of human urine and sera samples, resulting in the discovery of a host of proteins previously unreported. These beads can also be used to remove host cell proteins from purified recombinant proteins or proteins purified from natural sources that are intended for human consumption. These proteins typically reach purities of the order of 98%: higher purities often become prohibitively expensive. Yet, if incubated with Combinatorial Peptide Ligand Libraries (CPLL), even these impurities can be effectively removed with minute losses of the main, valuable product.

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Stewart-McGuinness, Callum, Christopher I. Platt, Matiss Ozols, Brian Goh, Tamara W. Griffiths, and Michael J. Sherratt. "Defining the Protease and Protease Inhibitor (P/PI) Proteomes of Healthy and Diseased Human Skin by Modified Systematic Review." Biomolecules 12, no. 3 (March 20, 2022): 475. http://dx.doi.org/10.3390/biom12030475.

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Proteases and protease inhibitors (P/PIs) are involved in many biological processes in human skin, yet often only specific families or related groups of P/PIs are investigated. Proteomics approaches, such as mass spectrometry, can define proteome signatures (including P/PIs) in tissues; however, they struggle to detect low-abundance proteins. To overcome these issues, we aimed to produce a comprehensive proteome of all P/PIs present in normal and diseased human skin, in vivo, by carrying out a modified systematic review using a list of P/PIs from MEROPS and combining this with key search terms in Web of Science. Resulting articles were manually reviewed against inclusion/exclusion criteria and a dataset constructed. This study identified 111 proteases and 77 protease inhibitors in human skin, comprising the serine, metallo-, cysteine and aspartic acid catalytic families of proteases. P/PIs showing no evidence of catalytic activity or protease inhibition, were designated non-peptidase homologs (NPH), and no reported protease inhibitory activity (NRPIA), respectively. MMP9 and TIMP1 were the most frequently published P/PIs and were reported in normal skin and most skin disease groups. Normal skin and diseased skin showed significant overlap with respect to P/PI profile; however, MMP23 was identified in several skin disease groups, but was absent in normal skin. The catalytic profile of P/PIs in wounds, scars and solar elastosis was distinct from normal skin, suggesting that a different group of P/PIs is responsible for disease progression. In conclusion, this study uses a novel approach to provide a comprehensive inventory of P/PIs in normal and diseased human skin reported in our database. The database may be used to determine either which P/PIs are present in specific diseases or which diseases individual P/PIs may influence.

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Mashini, Amirhossein Gheitanchi, Clinton A. Oakley, Sandeep S. Beepat, Lifeng Peng, Arthur R. Grossman, Virginia M. Weis, and Simon K. Davy. "The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum." Microorganisms 11, no. 2 (January 22, 2023): 292. http://dx.doi.org/10.3390/microorganisms11020292.

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The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian–dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography–mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana (‘Aiptasia’). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host–endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian–dinoflagellate symbiosis.

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Mulakala, Bharath, Katherine Smith, Miriam A. Snider, Mallory Honan, Ariel Ayers, and Sabrina L. Greenwood. "PSIX-4 Rumen Microbial Meta-Proteome and Milk Whey Proteome in Holstein Cows fed with High Starch and low Fiber Diet." Journal of Animal Science 100, Supplement_3 (September 21, 2022): 365–66. http://dx.doi.org/10.1093/jas/skac247.667.

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Abstract Identifying milk biomarkers impacted by dietary starch and fiber profiles can support optimization of feeding and concurrent promotion of animal health. The objective of this study was to characterize the rumen meta-proteome and milk whey proteome in Holstein cows fed different levels of physically effective undigestible NDF (peuNDF240) and rumen fermentable starch (RFS). Eight ruminally cannulated Holstein cows were included in a 4 x 4 Latin square design with four 28-day periods. From this study, samples were collected from cows in each period receiving one of two dietary treatments: 1) low peuNDF240, high RFS (LNHR) or 2) high peuNDF240, low RFS (HNLR). Rumen fluid and milk samples were collected at the end of each period at three timepoints, snap-frozen, and stored at -800C. Rumen microbial proteins and milk whey proteins were isolated, quantified, isobarically labeled, and analyzed by LC-MS/MS. The acquired product ion spectra from rumen fluid and the milk samples were searched against 71 composite databases and a cattle database, respectively. Data were analyzed using the PROC MIXED procedure in SAS 9.4. Of the 130 rumen-associated proteins identified across 22 searched microbial species, the abundances of 13 proteins were impacted by diet across eight microbial species. Six of these proteins were associated with core metabolism. Among the 159 quantified milk proteins, the abundances of 17 proteins were impacted by diet. Many of these proteins were associated with host defense, nutrient synthesis, and transportation. The abundance of CD14 and lactadherin was less with the LNHR diet (P < 0.05), whereas Prostaglandin-H2 D-isomerase and lipoprotein lipase abundances were greater with LNHR diet (P < 0.05). Our results indicate feeding a higher concentration of RFS has a greater influence on milk whey proteome than the rumen meta-proteome profile and highlight the potential use of milk whey proteins as biomarkers indicative of nutrition.

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Journal articles on the topic 'Low-abundance proteome'

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