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Journal articles on the topic 'Serum Proteomics'

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Author: Grafiati

Published: 6 September 2023

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1

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

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

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2

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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Arderiu, Gemma, Guiomar Mendieta, Alex Gallinat, Carmen Lambert, Alberto Díez-Caballero, Carlos Ballesta, and Lina Badimon. "Type 2 Diabetes in Obesity: A Systems Biology Study on Serum and Adipose Tissue Proteomic Profiles." International Journal of Molecular Sciences 24, no. 1 (January 3, 2023): 827. http://dx.doi.org/10.3390/ijms24010827.

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Obesity is associated with metabolic disorders such as insulin resistance and type 2 diabetes mellitus (T2DM), further increasing an already heightened cardiovascular risk. Here, amongst obese class III bariatric surgery patients, we have investigated the effect of T2DM in serum and in two, same patient, adipose tissue (AT) depots through proteomic profile expression analyses. Serum and AT samples from subcutaneous (SAT) and visceral (VAT) fat were collected during bariatric surgery. Bead-based targeted multiplex assay systems were used to simultaneously detect and quantify multiple targets in serum samples (targeted proteomics) and analyze changes in adipokine serum composition. AT samples were assessed through an untargeted proteomics approach. Through a systems biology analysis of the proteomic data, information on the affected biological pathways was acquired. In obese class III individuals, the presence of T2DM induced a significantly higher systemic release of ghrelin, GLP-1, glucagon, MMP3, BAFF, chitinase 3-like 1, TNF-R1 and TNF-R2, and a lower systemic release of IL-8. SAT and VAT proteomes belonging to the same patient showed significant differences in local protein content. While the proteins upregulated in VAT were indicative of metabolic dysregulation, SAT protein upregulation suggested adequate endocrine regulation. The presence of T2DM significantly affected VAT protein composition through the upregulation of dysregulating metabolic pathways, but SAT protein composition was not significantly modified. Our results show that T2DM induces metabolic dysregulation in obese individuals with changes in systemic marker levels and impairment of proteostasis in VAT but not in SAT.

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4

Issaq, Haleem J., Zhen Xiao, and Timothy D. Veenstra. "Serum and Plasma Proteomics." Chemical Reviews 107, no. 8 (August 2007): 3601–20. http://dx.doi.org/10.1021/cr068287r.

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Hohn, Andreas, Ivan Iovino, Fabrizio Cirillo, Hendrik Drinhaus, Kathrin Kleinbrahm, Lennert Boehm, Edoardo De Robertis, and Jochen Hinkelbein. "Bioinformatical Analysis of Organ-Related (Heart, Brain, Liver, and Kidney) and Serum Proteomic Data to Identify Protein Regulation Patterns and Potential Sepsis Biomarkers." BioMed Research International 2018 (March 21, 2018): 1–11. http://dx.doi.org/10.1155/2018/3576157.

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During the last years, proteomic studies have revealed several interesting findings in experimental sepsis models and septic patients. However, most studies investigated protein alterations only in single organs or in whole blood. To identify possible sepsis biomarkers and to evaluate the relationship between protein alteration in sepsis affected organs and blood, proteomics data from the heart, brain, liver, kidney, and serum were analysed. Using functional network analyses in combination with hierarchical cluster analysis, we found that protein regulation patterns in organ tissues as well as in serum are highly dynamic. In the tissue proteome, the main functions and pathways affected were the oxidoreductive activity, cell energy generation, or metabolism, whereas in the serum proteome, functions were associated with lipoproteins metabolism and, to a minor extent, with coagulation, inflammatory response, and organ regeneration. Proteins from network analyses of organ tissue did not correlate with statistically significantly regulated serum proteins or with predicted proteins of serum functions. In this study, the combination of proteomic network analyses with cluster analyses is introduced as an approach to deal with high-throughput proteomics data to evaluate the dynamics of protein regulation during sepsis.

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6

Shirai, Kumiko, Hayato Hikita, Sadatsugu Sakane, Ryohei Narumi, Jun Adachi, Akira Doi, Satoshi Tanaka, et al. "Serum amyloid P component and pro-platelet basic protein in extracellular vesicles or serum are novel markers of liver fibrosis in chronic hepatitis C patients." PLOS ONE 17, no. 7 (July 7, 2022): e0271020. http://dx.doi.org/10.1371/journal.pone.0271020.

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Extracellular vesicles (EVs) contain proteins, mRNAs, and microRNAs, and their cargos have emerged as novel diagnostic markers in various diseases. We aimed to discover novel and noninvasive biomarkers of liver fibrosis by proteomic analysis using serum EVs in patients with chronic hepatitis C. We performed shotgun proteomics using serum EVs isolated from 54 patients with histologically assessed liver fibrosis. Shotgun proteomics identified a total of 974 proteins, and 445 proteins were detected in more than half of the patients. Among them, a total of 9 proteins were identified as proteins that tended to increase or decrease with liver fibrosis with a significance of p<0.005 and that were different between F1-2 patients and F3-4 patients with a significance of p<0.01. Among the 9 proteins, targeted proteomics using serum EVs isolated from the sera of another 80 patients with histologically assessed liver fibrosis verified that serum amyloid P component (SAP) and pro-platelet basic protein (PPBP) levels in EVs significantly decreased with the progression of liver fibrosis and were significantly lower in F3-4 patients than in F1-2 patients. The diagnostic accuracies of SAP and PPBP in EVs for the liver fibrosis stage were comparable to those of type IV collagen 7S, hyaluronic acid, and the fibrosis-4 index (FIB-4 index). Moreover, serum SAP and PPBP levels correlated with the levels in EVs, and the ability of serum SAP and PPBP to diagnose liver fibrosis stage was also comparable to the abilities of type IV collagen 7S, hyaluronic acid, and the FIB-4 index. In conclusion, proteomic analysis of serum EVs identified SAP and PPBP as candidate biomarkers for predicting liver fibrosis in patients with chronic hepatitis C. In addition, SAP and PPBP levels in serum are strongly correlated with those in EVs and could represent markers of liver fibrosis.

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7

Lee, Pey Yee, Junaida Osman, Teck Yew Low, and Rahman Jamal. "Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery." Bioanalysis 11, no. 19 (October 2019): 1799–812. http://dx.doi.org/10.4155/bio-2019-0145.

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Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.

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8

Cottingham, Katie. "Research Profile: Mouse serum proteomics." Journal of Proteome Research 4, no. 5 (October 2005): 1481. http://dx.doi.org/10.1021/pr050525w.

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9

Kawada, Norifumi. "Cancer Serum Proteomics in Gastroenterology." Gastroenterology 130, no. 6 (May 2006): 1917–19. http://dx.doi.org/10.1053/j.gastro.2006.03.029.

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10

ANGI, M., BE DAMATO, and SE COUPLAND. "Serum proteomics in uveal melanoma." Acta Ophthalmologica 88 (September 2010): 0. http://dx.doi.org/10.1111/j.1755-3768.2010.3263.x.

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11

Liu, Wentao, Qiumeng Yang, Bingya Liu, and Zhenggang Zhu. "Serum proteomics for gastric cancer." Clinica Chimica Acta 431 (April 2014): 179–84. http://dx.doi.org/10.1016/j.cca.2014.02.001.

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12

Park, Yeonggyeong, Min Jeong Kim, Yoonhee Choi, Na Hyun Kim, Leeseul Kim, Seung Pyo Daniel Hong, Hyung-Gyo Cho, Emma Yu, and Young Kwang Chae. "Role of mass spectrometry-based serum proteomics signatures in predicting clinical outcomes and toxicity in patients with cancer treated with immunotherapy." Journal for ImmunoTherapy of Cancer 10, no. 3 (March 2022): e003566. http://dx.doi.org/10.1136/jitc-2021-003566.

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Immunotherapy has fundamentally changed the landscape of cancer treatment. However, only a subset of patients respond to immunotherapy, and a significant portion experience immune-related adverse events (irAEs). In addition, the predictive ability of current biomarkers such as programmed death-ligand 1 (PD-L1) remains unreliable and establishing better potential candidate markers is of great importance in selecting patients who would benefit from immunotherapy. Here, we focus on the role of serum-based proteomic tests in predicting the response and toxicity of immunotherapy. Serum proteomic signatures refer to unique patterns of proteins which are associated with immune response in patients with cancer. These protein signatures are derived from patient serum samples based on mass spectrometry and act as biomarkers to predict response to immunotherapy. Using machine learning algorithms, serum proteomic tests were developed through training data sets from advanced non-small cell lung cancer (Host Immune Classifier, Primary Immune Response) and malignant melanoma patients (PerspectIV test). The tests effectively stratified patients into groups with good and poor treatment outcomes independent of PD-L1 expression. Here, we review current evidence in the published literature on three liquid biopsy tests that use biomarkers derived from proteomics and machine learning for use in immuno-oncology. We discuss how these tests may inform patient prognosis as well as guide treatment decisions and predict irAE of immunotherapy. Thus, mass spectrometry-based serum proteomics signatures play an important role in predicting clinical outcomes and toxicity.

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Paul, Joseph, and Timothy D. Veenstra. "Separation of Serum and Plasma Proteins for In-Depth Proteomic Analysis." Separations 9, no. 4 (April 1, 2022): 89. http://dx.doi.org/10.3390/separations9040089.

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There are probably no biological samples that did more to spur interest in proteomics than serum and plasma. The belief was that comparing the proteomes of these samples obtained from healthy and disease-affected individuals would lead to biomarkers that could be used to diagnose conditions such as cancer. While the continuing development of mass spectrometers with greater sensitivity and resolution has been invaluable, the invention of strategic strategies to separate circulatory proteins has been just as critical. Novel and creative separation techniques were required because serum and plasma probably have the greatest dynamic range of protein concentration of any biological sample. The concentrations of circulating proteins can range over twelve orders of magnitude, making it a challenge to identify low-abundance proteins where the bulk of the useful biomarkers are believed to exist. The major goals of this article are to (i) provide an historical perspective on the rapid development of serum and plasma proteomics; (ii) describe various separation techniques that have made obtaining an in-depth view of the proteome of these biological samples possible; and (iii) describe applications where serum and plasma proteomics have been employed to discover potential biomarkers for pathological conditions.

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14

Rossi, Giacomo, Alessandra Gavazza, Silvia Vincenzetti, Sara Mangiaterra, Livio Galosi, Andrea Marchegiani, Graziano Pengo, Gianni Sagratini, Massimo Ricciutelli, and Matteo Cerquetella. "Clinicopathological and Fecal Proteome Evaluations in 16 Dogs Presenting Chronic Diarrhea Associated with Lymphangiectasia." Veterinary Sciences 8, no. 10 (October 19, 2021): 242. http://dx.doi.org/10.3390/vetsci8100242.

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Canine intestinal lymphangiectasia (IL) is a condition characterized by variably severe gastrointestinal signs, frequently associated with laboratory abnormalities; the research for markers allowing a better understanding of the severity degree and/or obtaining an early diagnosis and/or monitoring is continuously progressing. In the present study, we investigated possible new diagnostic/follow-up markers in IL dogs, namely, serum C-reactive protein, serum bacterial lipopolysaccharide, serum cleaved cytokeratin 18, serum citrulline, and zonulin (in both serum and feces). A fecal proteomic study looking for possible confirmation and/or new marker candidates was also performed. All markers in both substrates, with the exception of serum citrulline, significantly differed between diseased and control dogs. Fecal proteomics allowed the retrieval of three proteins in IL dogs (Fc fragment of IgG-binding protein; transthyretin; proproteinase E) that were not previously found in clinically healthy subjects. Although further studies are needed, C-reactive protein, bacterial lipopolysaccharide, cleaved cytokeratin 18, and zonulin (in both serum and feces) resulted as promising markers for canine IL; similarly, fecal proteomics represents a road worthy of being pursued in the search for candidate biomarkers.

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Dunphy, Katie, Kelly O’Mahoney, Paul Dowling, Peter O’Gorman, and Despina Bazou. "Clinical Proteomics of Biofluids in Haematological Malignancies." International Journal of Molecular Sciences 22, no. 15 (July 27, 2021): 8021. http://dx.doi.org/10.3390/ijms22158021.

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Since the emergence of high-throughput proteomic techniques and advances in clinical technologies, there has been a steady rise in the number of cancer-associated diagnostic, prognostic, and predictive biomarkers being identified and translated into clinical use. The characterisation of biofluids has become a core objective for many proteomic researchers in order to detect disease-associated protein biomarkers in a minimally invasive manner. The proteomes of biofluids, including serum, saliva, cerebrospinal fluid, and urine, are highly dynamic with protein abundance fluctuating depending on the physiological and/or pathophysiological context. Improvements in mass-spectrometric technologies have facilitated the in-depth characterisation of biofluid proteomes which are now considered hosts of a wide array of clinically relevant biomarkers. Promising efforts are being made in the field of biomarker diagnostics for haematologic malignancies. Several serum and urine-based biomarkers such as free light chains, β-microglobulin, and lactate dehydrogenase are quantified as part of the clinical assessment of haematological malignancies. However, novel, minimally invasive proteomic markers are required to aid diagnosis and prognosis and to monitor therapeutic response and minimal residual disease. This review focuses on biofluids as a promising source of proteomic biomarkers in haematologic malignancies and a key component of future diagnostic, prognostic, and disease-monitoring applications.

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Sharma, Vipin Kumar, and Ravi Kumar. "Current applications of proteomics: a key and novel approach." International Journal of Advances in Medicine 6, no. 6 (November 25, 2019): 1953. http://dx.doi.org/10.18203/2349-3933.ijam20195259.

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Proteomics represented vital applications of technologies in the identification and quantification of high to moderate proteins (cellular signalling networks) found in biological matrix such as tissues, cells and fluids. Proteomics based technical knowledge is applied and verified in several preclinical research settings such as invention of diagnostic markers for specific disease and have shown to be increased in clinical applications. Extensive studies on proteomics resulted in detection of biomarkers that have been highly advanced in using diseases for cancer, lungs, cardiovascular, renal and neuro-regenerative and Parkinson's disease by introducing human origins for biocompatibility such as urine and serum. Advancement in the proteomic methods is conferring candidate right direction for clinical usage. In this review, recent developments and widely used proteomics approaches such as Mass Spectrometry (MS), Microarray chips are elaborately addressed and also focused merits and demerits of commonly used advanced approaches such as Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and Data Independent Acquisition (DIA) and other used proteomics and that roles, in order to aid clinicians, were also discussed in the light of biomedical applications.

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Barelli, Stefano, David Crettaz, Lynne Thadikkaran, Olivier Rubin, and Jean-Daniel Tissot. "Plasma/serum proteomics: pre-analytical issues." Expert Review of Proteomics 4, no. 3 (June 2007): 363–70. http://dx.doi.org/10.1586/14789450.4.3.363.

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18

Carbone, D. "SP141 Serum proteomics in lung cancer." European Journal of Cancer Supplements 7, no. 4 (October 2009): 1–2. http://dx.doi.org/10.1016/s1359-6349(09)72106-8.

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19

Yu, Li-Rong, Ming Zhou, Thomas P. Conrads, and Timothy D. Veenstra. "Diagnostic Proteomics: Serum Proteomic Patterns for the Detection of Early Stage Cancers." Disease Markers 19, no. 4-5 (2004): 209–18. http://dx.doi.org/10.1155/2004/612071.

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The ability to interrogate thousands of proteins found in complex biological samples using proteomic technologies has brought the hope of discovering novel disease-specific biomarkers. While most proteomic technologies used to discover diagnostic biomarkers are quite sophisticated, "proteomic pattern analysis" has emerged as a simple, yet potentially revolutionary, method for the early diagnosis of diseases. Utilizing this technology, hundreds of clinical samples can be analyzed per day and several preliminary studies suggest proteomic pattern analysis has the potential to be a novel, highly sensitive diagnostic tool for the early detection of cancer.

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20

Vidal, Bernardo C., Joseph V. Bonventre, and Stephen I-Hong Hsu. "Towards the application of proteomics in renal disease diagnosis." Clinical Science 109, no. 5 (October 24, 2005): 421–30. http://dx.doi.org/10.1042/cs20050085.

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Proteomics is widely envisioned as playing a significant role in the translation of genomics to clinically useful applications, especially in the areas of diagnostics and prognostics. In the diagnosis and treatment of kidney disease, a major priority is the identification of disease-associated biomarkers. Proteomics, with its high-throughput and unbiased approach to the analysis of variations in protein expression patterns (actual phenotypic expression of genetic variation), promises to be the most suitable platform for biomarker discovery. Combining such classic analytical techniques as two-dimensional gel electrophoresis with more sophisticated techniques, such as MS, has enabled considerable progress to be made in cataloguing and quantifying proteins present in urine and various kidney tissue compartments in both normal and diseased physiological states. Despite these accomplishments, there remain a number of important challenges that will need to be addressed in order to pave the way for the universal acceptance of proteomics as a clinically relevant diagnostic tool. We discuss issues related to three such critical developmental tasks as follows: (i) completely defining the proteome in the various biological compartments (e.g. tissues, serum and urine) in both health and disease, which presents a major challenge given the dynamic range and complexity of such proteomes; (ii) achieving the routine ability to accurately and reproducibly quantify proteomic expression profiles; and (iii) developing diagnostic platforms that are readily applicable and technically feasible for use in the clinical setting that depend on the fruits of the preceding two tasks to profile multiple disease biomarkers.

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21

Alsoud, D., P. Sudhakar, J. Sabino, M. Ferrante, B. Verstockt, and S. Vermeire. "DOP08 Serum proteomics predict endoscopic remission in patients with Crohn’s Disease." Journal of Crohn's and Colitis 15, Supplement_1 (May 1, 2021): S046—S047. http://dx.doi.org/10.1093/ecco-jcc/jjab073.047.

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Abstract Background Recent progress in deciphering the complex pathogenesis of Crohn’s disease (CD) has yielded several effective biologicals. However, ambitious therapeutic goals remain unfulfilled as almost 30% of patients are primary non-responders to a particular biological. This underscores the need for easy-to-implement biomarkers that predict (non-)remission. We aimed to identify serum protein biomarkers that predict endoscopic remission in CD patients. Methods Serum samples from 169 consecutive CD patients with active endoscopic disease (presence of ulcerations) before starting a biological [infliximab (IFX), adalimumab (ADA), vedolizumab (VDZ) or ustekinumab (UST)] to which they were naïve were collected. Patients were prospectively followed with endoscopic re-assessment after 6–12 months. There were 102 patients (Table 1) with endoscopic remission (SES ≤ 2 or disappearance of all ulcers), whereas 67 showed no improvement. Two independent and complementary proteomic platforms were used: 644 proteins belonging to predesigned assays were quantified using Proximity Extension Assay (PEA) technology (Olink Proteomics AB, Sweden). Second, wide protein discovery mass spectrometry (MS)-based technic (Caprion, Canada) was used and quantified another 985 proteins. A multivariate modelling framework was then applied on a randomly selected training sub-cohort (85%). Predictive performance of identified panels was assessed on the remaining test sub-cohort (15%). We sought to implement the same framework on the drug-specific subgroups; however, train/test splitting was not possible in IFX or ADA subgroups due to very few observations in the non-remission arms which diminishes the possibility for reliable predictive modelling. Results Applying the modelling framework on training sets from the general cohort, VDZ subgroup and UST subgroup, proteomic panels were selected and consisted of 26, 6 and 8 proteins, respectively, and showed high performance in the test sets (Table 2). VDZ and UST panels shared only 2 proteins each with the general panel, and had no predictive power (accuracy ≤ 0.5) when used to predict other subgroups, making them specific to their respective drugs. Selected proteins are involved among others in pro-inflammatory, extracellular matrix modelling, coagulation and cellular-vascular interaction pathways (Table 3). Conclusion Applying a multivariate machine learning algorithm on a wide pool of serum proteomics analysed through two discovery technics, we were able to identify 3 proteomic panels that can predict endoscopic (non)remission in patients with CD. Exact implication of these proteins in intestinal inflammation and a validation in an independent cohort is being further investigated.

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Rešetar Maslov, Dina, Vladimir Farkaš, Ivana Rubić, Josipa Kuleš, Anđelo Beletić, Blanka Beer Ljubić, Iva Šmit, Vladimir Mrljak, and Marin Torti. "Serum Proteomic Profiles Reflect the Stages of Myxomatous Mitral Valve Disease in Dogs." International Journal of Molecular Sciences 24, no. 8 (April 12, 2023): 7142. http://dx.doi.org/10.3390/ijms24087142.

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Canine myxomatous mitral valve disease (MMVD) is similar to Barlow’s form of MMVD in humans. These valvulopathies are complex, with varying speeds of progression. We hypothesized that the relative abundances of serum proteins would help identify the consecutive MMVD stages and discover new disease pathways on a systemic level. To identify distinction-contributing protein panels for disease onset and progression, we compared the proteomic profiles of serum from healthy dogs and dogs with different stages of naturally occurring MMVD. Dogs were divided into experimental groups on the basis of the left-atrium-to-aorta ratio and normalized left ventricular internal dimension in diastole values. Serum was collected from healthy (N = 12) dogs, dogs diagnosed with MMVD in stages B1 (N = 13) and B2 (N = 12) (asymptomatic), and dogs diagnosed with MMVD in chronic stage C (N = 13) (symptomatic). Serum biochemistry and selected ELISAs (galectin-3, suppression of tumorigenicity, and asymmetric dimethylarginine) were performed. Liquid chromatography–mass spectrometry (LC–MS), tandem mass tag (TMT) quantitative proteomics, and statistical and bioinformatics analysis were employed. Most of the 21 serum proteins with significantly different abundances between experimental groups (p < 0.05, FDR ˂ 0.05) were classified as matrix metalloproteinases, protease inhibitors, scaffold/adaptor proteins, complement components, anticoagulants, cytokine, and chaperone. LC–MS TMT proteomics results obtained for haptoglobin, clusterin, and peptidase D were further validated analytically. Canine MMVD stages, including, for the first time, asymptomatic B1 and B2 stages, were successfully distinguished in dogs with the disease and healthy dogs on the basis of the relative abundances of a panel of specific serum proteins. Most proteins with significantly different abundances were involved in immune and inflammatory pathways. Their role in structural remodeling and progression of canine MMVD must be further investigated. Further research is needed to confirm the resemblance/difference with human MMVD. Proteomics data are available via ProteomeXchange with the unique dataset identifier PXD038475.

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Blatt, Sebastian, Peer W. Kämmerer, Maximilian Krüger, Rambabu Surabattula, Daniel G. E. Thiem, Simon T. Dillon, Bilal Al-Nawas, Towia A. Libermann, and Detlef Schuppan. "High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma." Cancers 15, no. 7 (March 30, 2023): 2071. http://dx.doi.org/10.3390/cancers15072071.

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Improved serological biomarkers are needed for the early detection, risk stratification and treatment surveillance of patients with oral squamous cell carcinoma (OSCC). We performed an exploratory study using advanced, highly specific, DNA-aptamer-based serum proteomics (SOMAscan, 1305-plex) to identify distinct proteomic changes in patients with OSCC pre- vs. post-resection and compared to healthy controls. A total of 63 significantly differentially expressed serum proteins (each p < 0.05) were found that could discriminate between OSCC and healthy controls with 100% accuracy. Furthermore, 121 proteins were detected that were significantly altered between pre- and post-resection sera, and 12 OSCC-associated proteins reversed to levels equivalent to healthy controls after resection. Of these, 6 were increased and 6 were decreased relative to healthy controls, highlighting the potential relevance of these proteins as OSCC tumor markers. Pathway analyses revealed potential pathophysiological mechanisms associated with OSCC. Hence, quantitative proteome analysis using SOMAscan technology is promising and may aid in the development of defined serum marker assays to predict tumor occurrence, progression and recurrence in OSCC, and to guide personalized therapies.

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Zhang, Zheyu, Wenbo Wang, Ling Jin, Xin Cao, Gonghui Jian, Ning Wu, Xia Xu, Ye Yao, and Dongsheng Wang. "iTRAQ-Based Quantitative Proteomics Analysis of the Protective Effect of Yinchenwuling Powder on Hyperlipidemic Rats." Evidence-Based Complementary and Alternative Medicine 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/3275096.

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Yinchenwuling powder (YCL) is an effective traditional Chinese medicine formula to modulate lipid levels. In this study, we established hyperlipidemic rat models and treated them with YCL. The serum concentrations of lipid, malondialdehyde (MDA), endothelin-1 (ET-1), and calcitonin gene-related peptide (CGRP) were measured. Adventitia-free vascular proteins between hyperlipidemic rats and YCL-treated rats were identified using iTRAQ-based quantitative proteomics research approach. Proteins with 1.3-fold difference were analyzed through bioinformatics, and proteomic results were verified by Western blot. The results showed that the serum levels of TC, TG, LDL-C, ET-1, and MDA were significantly decreased, whereas the HDL-C and CGRP levels were significantly increased in the YCL-treated group. Proteomics technology identified 4,382 proteins, and 15 proteins were selected on the basis of their expression levels and bioinformatics. Of these proteins, 2 (Adipoq and Gsta1) were upregulated and 13 (C3, C4, C6, Cfh, Cfp, C8g, C8b, Lgals1, Fndc1, Fgb, Fgg, Kng1, and ApoH) were downregulated in the YCL-treated rats. Their functions were related to immunity, inflammation, coagulation and hemostasis, oxidation and antioxidation, and lipid metabolism and transport. The validated results of ApoH were consistent with the proteomics results. This study enhanced our understanding on the therapeutic effects and mechanism of YCL on hyperlipidemia.

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Benabdelkamel, Hicham, Hanadi Alamri, Meshail Okla, Afshan Masood, Mai Abdel Jabar, Ibrahim O. Alanazi, Assim A. Alfadda, Imran Nizami, Majed Dasouki, and Anas M. Abdel Rahman. "Serum-Based Proteomics Profiling in Adult Patients with Cystic Fibrosis." International Journal of Molecular Sciences 21, no. 19 (October 8, 2020): 7415. http://dx.doi.org/10.3390/ijms21197415.

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Cystic fibrosis (CF), the most common lethal autosomal recessive disorder among Caucasians, is caused by mutations in the CF transmembrane conductance regulator (CFTR) chloride channel gene. Despite significant advances in the management of CF patients, novel disease-related biomarkers and therapies must be identified. We performed serum proteomics profiling in CF patients (n = 28) and healthy subjects (n = 10) using the 2D-DIGE MALDI-TOF proteomic approach. Out of a total of 198 proteins identified, 134 showed a statistically significant difference in abundance and a 1.5-fold change (ANOVA, p < 0.05), including 80 proteins with increased abundance and 54 proteins with decreased abundance in CF patients. A multiple reaction monitoring-mass spectrometry analysis of six differentially expressed proteins identified by a proteomic approach (DIGE-MALD-MS) showed a significant increase in C3 and CP proteins and a decrease in APOA1, Complement C1, Hp, and RBP4proteins compared with healthy controls. Fifteen proteins were identified as potential biomarkers for CF diagnosis. An ingenuity pathway analysis of the differentially regulated proteins indicates that the central nodes dysregulated in CF subjects involve pro-inflammatory cytokines, ERK1/2, and P38 MAPK, which are primarily involved in catalytic activities and metabolic processes. The involved canonical pathways include those related to FXR/RXR, LXR/RXR, acute phase response, IL12, nitric oxide, and reactive oxygen species in macrophages. Our data support the current efforts toward augmenting protease inhibitors in patients with CF. Perturbations in lipid and vitamin metabolism frequently observed in CF patients may be partly due to abnormalities in their transport mechanism.

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Schwenk, Jochen M., Marcus Gry, Rebecca Rimini, Mathias Uhlén, and Peter Nilsson. "Antibody Suspension Bead Arrays within Serum Proteomics." Journal of Proteome Research 7, no. 8 (August 2008): 3168–79. http://dx.doi.org/10.1021/pr700890b.

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Rosenblatt, Kevin P., Peter Bryant-Greenwood, J. Keith Killian, Arpita Mehta, David Geho, Virginia Espina, Emanuel F. Petricoin, and Lance A. Liotta. "Serum Proteomics in Cancer Diagnosis and Management." Annual Review of Medicine 55, no. 1 (February 2004): 97–112. http://dx.doi.org/10.1146/annurev.med.55.091902.105237.

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Meric-Bernstam, Funda. "Serum Proteomics for BRCA1-associated Breast Cancer." Annals of Surgical Oncology 11, no. 10 (October 2004): 883–84. http://dx.doi.org/10.1245/aso.2004.08.909.

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Tremlett, Helen, Darlene L. Y. Dai, Zsuzsanna Hollander, Anita Kapanen, Tariq Aziz, Janet E. Wilson-McManus, Scott J. Tebbutt, Christoph H. Borchers, Joel Oger, and Gabriela V. Cohen Freue. "Serum proteomics in multiple sclerosis disease progression." Journal of Proteomics 118 (April 2015): 2–11. http://dx.doi.org/10.1016/j.jprot.2015.02.018.

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Somasundaram, Kumaravel, Mamatha B. Nijaguna, and Durairaj Mohan Kumar. "Serum proteomics of glioma: methods and applications." Expert Review of Molecular Diagnostics 9, no. 7 (October 2009): 695–707. http://dx.doi.org/10.1586/erm.09.52.

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IJsselstijn, Linda, Janne M. Papma, Lennard J. M. Dekker, Wim Calame, Christoph Stingl, Peter J. Koudstaal, Niels D. Prins, Peter A. E. Sillevis Smitt, and Theo M. Luider. "Serum proteomics in amnestic mild cognitive impairment." PROTEOMICS 13, no. 16 (July 19, 2013): 2526–33. http://dx.doi.org/10.1002/pmic.201200190.

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Zougman, Alexandre, John P. Wilson, and Rosamonde E. Banks. "A simple serum depletion method for proteomics analysis." BioTechniques 69, no. 2 (August 2020): 148–51. http://dx.doi.org/10.2144/btn-2020-0017.

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Serum is the body fluid most often used in biomarker discovery. Albumin, the most abundant serum protein, contributes approximately 50% of the serum protein content, with an additional dozen abundant proteins dominating the rest of the serum proteome. To profile this challenging protein mixture by proteomics, the abundant proteins must be depleted to allow for detection of the low-abundant proteins, the primary biomarker targets. Current serum depletion approaches for proteomics are costly and relatively complex to couple with protein digestion. We demonstrate a simple, affordable serum depletion methodology that, within a few minutes of processing, results in two captured serum fractions – albumin-depleted and albumin-rich – which are digested in situ. We believe our method is a useful addition to the biomarker sample preparation toolbox.

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Stakhneva, Ekaterina M., Irina A. Meshcheryakova, Evgeny A. Demidov, Konstantin V. Starostin, Evgeny V. Sadovski, Sergey E. Peltek, Michael I. Voevoda, Alexander M. Chernyavskii, Alexander M. Volkov, and Yuliya I. Ragino. "A Proteomic Study of Atherosclerotic Plaques in Men with Coronary Atherosclerosis." Diagnostics 9, no. 4 (November 7, 2019): 177. http://dx.doi.org/10.3390/diagnostics9040177.

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Background: To study the changes in protein composition of atherosclerotic plaques at different stages of their development in coronary atherosclerosis using proteomics. Methods: The object of research consisted of homogenates of atherosclerotic plaques from coronary arteries at different stages of development, obtained from 15 patients. Plaque proteins were separated by two-dimensional electrophoresis. The resultant protein spots were identified by the matrix-assisted laser desorption ionization method with peptide mass mapping. Results: Groups of differentially expressed proteins, in which the amounts of proteins differed more than twofold (p < 0.05), were identified in pools of homogenates of atherosclerotic plaques at three stages of development. The amounts of the following proteins were increased in stable atherosclerotic plaques at the stage of lipidosis and fibrosis: vimentin, tropomyosin β-chain, actin, keratin, tubulin β-chain, microfibril-associated glycoprotein 4, serum amyloid P-component, and annexin 5. In plaques at the stage of fibrosis and calcification, the amounts of mimecan and fibrinogen were increased. In unstable atherosclerotic plaque of the necrotic–dystrophic type, the amounts of human serum albumin, mimecan, fibrinogen, serum amyloid P-component and annexin were increased. Conclusion: This proteomic study identifies the proteins present in atherosclerotic plaques of coronary arteries by comparing their proteomes at three different stages of plaque development during coronary atherosclerosis.

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Orwoll, Eric, Jack Wiedrick, Steven R. Cummings, Dan Evans, Wanlin Zheng, Cory Funk, Nathan Price, and Jodi Lapidus. "THE PROTEOMICS OF LONGEVITY." Innovation in Aging 3, Supplement_1 (November 2019): S209. http://dx.doi.org/10.1093/geroni/igz038.760.

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Abstract The biological underpinnings of longevity are poorly elucidated in humans. We used a novel, high-throughput discovery-proteomics approach to identify serum proteins associated with longevity (living beyond 90th percentile of survival) in community-dwelling men age ≥65 years in the MrOs Study. Baseline serum from 2473 men was analyzed using liquid chromatography-ion mobility-mass spectrometry. >21,000 peptides and 2931 proteins were recognized. Twenty-five proteins significantly associated with attainment of longevity over 15 yrs of observation were identified using rigorous statistical methods. 25 proteins were significantly associated; all were lower in long lived men than in men dying earlier. Most longevity-associated proteins were from inflammatory pathways; some have multifunctional biological roles potentially reflecting other mechanisms. Pathway analyses suggest important upstream regulators may be causally responsible for the associations. These results provide the opportunity to evaluate these proteins as biomarkers, and highlight the potential importance of their biological pathways in the origins of long life.

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Eckersall, David. "321 ASAS-EAAP Talk: Quantitative proteomics in animal and veterinary science: a pipeline for exploiting advanced analytical technology." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 55–56. http://dx.doi.org/10.1093/jas/skaa278.100.

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Abstract Application of proteomic investigation to veterinary and animal sciences has grown over the last decade, but has still not reached its full potential of application in animal health and production research [1]. Nevertheless, establishing a versatile methodology has allowed the application of quantitative proteomics for increased understanding of physiological and pathophysiological challenges, and especially to identify potential biomarkers of disease in a range of animal species. A pipeline of sample preparation and mass spectrometry followed by statistical, bioinformatic and biochemical analyses has been established to deal with biofluids and tissue samples from cattle, sheep, pigs, chickens, dogs and cats as well as wild animals. Quantitative proteomic investigation of milk in an experimental model of Streptococcus uberis mastitis of dairy cows has identified potential novel biomarkers with implications for diagnosis and treatment of this major disease. Proteins in milk which have potential as disease biomarkers, such as cathelicidin, haptoglobin and mammary associated serum amyloid A3, are significantly increased in abundance during bovine mastitis. Proteomic investigation has confirmed that these biomarkers are also increased in milk during subclinical and clinical mastitis. Proteomic analysis of plasma from chicken following stimulation of the inflammatory response to Escherichia coli lipopolysaccharide endotoxin has characterised major changes in the chicken plasma proteome. Novel biomarker candidates of hemopexin and fatty acid binding protein have been identified. This proteomic pipeline can be incorporated into many areas of research, providing novel findings at the forefront of animal and veterinary science. Such proteomic investigation requires close interdisciplinary collaboration between experts in mass spectrometry, bioinformatics, statistics and animal production in order to fully exploit recent technological advances in the omic sciences.[1] P. Bilic, et al, Proteomics in Veterinary Medicine and Animal Science: Neglected Scientific Opportunities with Immediate Impact, Proteomics. 47 (2018) 1–7. doi:10.1002/pmic.201800047.

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Zhang, Ruohan, Minglin Ou, Yue Zhang, Qiang Yan, Huaizhou Chen, Liusheng Lai, Ying Li, et al. "Comparative proteomic analysis of human serum before and after liver transplantation using quantitative proteomics." Oncotarget 10, no. 26 (April 2, 2019): 2508–14. http://dx.doi.org/10.18632/oncotarget.26761.

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Katsafadou, Angeliki I., Natalia G. C. Vasileiou, and George C. Fthenakis. "Use of Proteomics in the Study of Mastitis in Ewes." Pathogens 8, no. 3 (August 29, 2019): 134. http://dx.doi.org/10.3390/pathogens8030134.

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The objective of this review is to describe the usage and applicability of proteomics technologies in the study of mastitis in ewes. In ewes, proteomics technologies have been employed for furthering knowledge in mastitis caused by various agents (Staphylococcus aureus, Staphylococcus chromogenes, Mannheimia haemolytica, Streptococcus uberis, Mycoplasma agalactiae). Studies have focused on improving knowledge regarding pathogenesis of the infections and identifying biomarkers for its diagnosis. Findings have revealed that ewes with mastitis mount a defence response, controlled by many proteins and over various mechanisms and pathways, which are interdependent at various points. Many proteins can participate in this process. Moreover, as the result of proteomics studies, cathelicidins and serum amyloid A have been identified as proteins that can be used as biomarkers for improved diagnosis of the disease. In the long term, proteomics will contribute to improvements in the elucidation of the pathogenesis of mastitis. Further in-depth investigations into the various proteomes and application of new methodological strategies in experimental and clinical studies will provide information about mastitis processes, which will be of benefit in controlling the disease. Improvement of diagnostic techniques, establishment of prognostic tools and development of vaccines are key areas for targeted research.

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Bell, Lauren N., Lydia Lee, Romil Saxena, Kerry G. Bemis, Mu Wang, Janice L. Theodorakis, Raj Vuppalanchi, Mouhamad Alloosh, Michael Sturek, and Naga Chalasani. "Serum proteomic analysis of diet-induced steatohepatitis and metabolic syndrome in the Ossabaw miniature swine." American Journal of Physiology-Gastrointestinal and Liver Physiology 298, no. 5 (May 2010): G746—G754. http://dx.doi.org/10.1152/ajpgi.00485.2009.

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We recently developed a nutritional model of steatohepatitis and metabolic syndrome in Ossabaw pigs. Here we describe changes in the serum proteome of pigs fed standard chow (control group; n = 7), atherogenic diet ( n = 5), or modified atherogenic diet (M-ath diet group; n = 6). Pigs fed atherogenic diet developed metabolic syndrome and mildly abnormal liver histology, whereas pigs fed M-ath diet exhibited severe metabolic syndrome and liver injury closely resembling human nonalcoholic steatohepatitis (NASH). Using a label-free mass spectrometry-based proteomics approach, we identified 1,096 serum proteins, 162 of which changed significantly between any two diet groups (false discovery rate <5%). Biological classification of proteins with significant changes revealed functions previously implicated in development of NASH in humans, including immune system regulation and inflammation (orosomucoid 1, serum amyloid P component, paraoxonase 1, protein similar to α-2-macroglobulin precursor, β-2-microglobulin, p101 protein, and complement components 2 and C8G), lipid metabolism (apolipoproteins C-III, E, E precursor, B, and N), structural and extracellular matrix proteins (transthyretin and endopeptidase 24.16 type M2), and coagulation [carboxypeptidase B2 (plasma)]. Several proteins with significant differential expression in pigs were also identified in our recent human proteomics study as changing significantly in serum from patients across the spectrum of nonalcoholic fatty liver disease, including apolipoproteins C-III and B, orosomucoid 1, serum amyloid P component, transthyretin, paraoxonase 1, and a protein similar to α-2-macroglobulin precursor. This serum proteomic analysis provides additional information about the pathogenesis of NASH and further characterizes our large animal model of diet-induced steatohepatitis and metabolic syndrome in Ossabaw pigs.

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Liu, Xiaoling, Yinghao Cao, Hongmei Fu, Jie Wei, Jianhong Chen, Jun Hu, and Bende Liu. "Proteomics Analysis of Serum from COVID-19 Patients." ACS Omega 6, no. 11 (March 9, 2021): 7951–58. http://dx.doi.org/10.1021/acsomega.1c00616.

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Li, Jianhua, Lin Lu, Xinping Xie, Xiaofeng Dai, Shan Zheng, and Lihong Chen. "Proteomics Analysis of Serum Proteins in Gestational Diabetes." Evidence-Based Complementary and Alternative Medicine 2021 (November 2, 2021): 1–8. http://dx.doi.org/10.1155/2021/4724590.

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Objective. The purpose of this study was to screen serum proteins for biomarkers of gestational diabetes mellitus (GDM) and to investigate its pathogenesis by analyzing the differences in serum proteomics between pregnant women with GDM and healthy pregnant women. Methods. Patients who were admitted to the First Affiliated Hospital of Fujian Medical University from June 2019 to January 2020 were included. According to the medical history and the results of the 75 g oral glucose tolerance test (OGTT), they were divided into the normal pregnant women group and GDM pregnant women group. The serum of two groups of patients was collected. High performance liquid chromatography-mass spectrometry was used to identify differentially expressed serum proteins between pregnant women with GDM and healthy pregnant women, and bioinformatics analysis was then performed on the identified proteins. Results. A total of 1152 quantifiable proteins were detected; among them, 15 were upregulated in serum of GDM pregnant women, while 26 were downregulated. The subsequent parallel reaction monitoring (PRM) assay validated the expression levels of 12 out of 41 differentially expressed proteins. Moreover, bioinformatics analysis revealed that the differentially expressed proteins are involved in multiple biological processes and signaling pathways related to the lipid metabolism, glycan degradation, immune response, and platelet aggregation. Conclusions. This study identified 41 serum proteins with differential expression between pregnant women with GDM and healthy pregnant women, providing new candidate molecules for elucidating GDM pathogenesis and screening therapeutic targets.

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Lausted, Christopher, Zhiyuan Hu, and Leroy Hood. "Quantitative Serum Proteomics from Surface Plasmon Resonance Imaging." Molecular & Cellular Proteomics 7, no. 12 (August 3, 2008): 2464–74. http://dx.doi.org/10.1074/mcp.m800121-mcp200.

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RAI, ALEX J., and DANIEL W. CHAN. "Cancer Proteomics: Serum Diagnostics for Tumor Marker Discovery." Annals of the New York Academy of Sciences 1022, no. 1 (June 2004): 286–94. http://dx.doi.org/10.1196/annals.1318.044.

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Chatterjee, Madhumita, Nancy K. Levin, Jay P. Shah, Alexei Ionan, Harry E. Grates, and Michael A. Tainsky. "Pathways to implementation of serum proteomics for cancer." Expert Opinion on Medical Diagnostics 1, no. 1 (September 2007): 3–15. http://dx.doi.org/10.1517/17530059.1.1.3.

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Abu-Asab, Mones, Mohamed Chaouchi, and Hakima Amri. "Phyloproteomics: What Phylogenetic Analysis Reveals about Serum Proteomics." Journal of Proteome Research 5, no. 9 (September 2006): 2236–40. http://dx.doi.org/10.1021/pr0504485.

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Bahtiyar, Mert Ozan, Ray Bahado-Singh, and Joshua A. Copel. "Serum Proteomics Distinguish Preeclamptic Women From Normal Women." Obstetrics & Gynecology 101, Supplement (April 2003): 82S. http://dx.doi.org/10.1097/00006250-200304001-00193.

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BAHTIYAR, M. "Serum proteomics distinguish preeclamptic women from normal women." Obstetrics & Gynecology 101, no. 4 (April 2003): S82. http://dx.doi.org/10.1016/s0029-7844(02)02953-8.

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Wang, Fengrong, Christyne Chmil, Frank Pierce, Kulothungan Ganapathy, Brooks B. Gump, James A. MacKenzie, Yehia Mechref, and Kestutis Bendinskas. "Immobilized metal affinity chromatography and human serum proteomics." Journal of Chromatography B 934 (September 2013): 26–33. http://dx.doi.org/10.1016/j.jchromb.2013.06.032.

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Qin, Danying, Wenxian Yang, Zeping Pan, Yuheng Zhang, Xueyong Li, and Sivalingam Lakshmanan. "Differential proteomics analysis of serum exosomein burn patients." Saudi Journal of Biological Sciences 27, no. 9 (September 2020): 2215–20. http://dx.doi.org/10.1016/j.sjbs.2020.06.024.

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Zhang, Ai-hua, Hui Sun, Guang-li Yan, Ying Han, and Xi-jun Wang. "Serum Proteomics in Biomedical Research: A Systematic Review." Applied Biochemistry and Biotechnology 170, no. 4 (April 23, 2013): 774–86. http://dx.doi.org/10.1007/s12010-013-0238-7.

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Lu, Qi, Chongdong Liu, Ye Liu, Nawei Zhang, Haiteng Deng, and Zhenyu Zhang. "Serum markers of pre-eclampsia identified on proteomics." Journal of Obstetrics and Gynaecology Research 42, no. 9 (June 8, 2016): 1111–18. http://dx.doi.org/10.1111/jog.13037.

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