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Human tear film protein sampling using soft contact lenses Clin. Proteom. (IF 3.8) Pub Date : 2024-03-13 Robert K. Roden, Nathan Zuniga, Joshua C. Wright, David H. Parkinson, Fangfang Jiang, Leena M. Patil, Rebecca S. Burlett, Alyssa A. Nitz, Joshua J. Rogers, Jarett T. Pittman, Kenneth L. Virgin, P. Christine Ackroyd, Samuel H. Payne, John C. Price, Kenneth A. Christensen
Human tear protein biomarkers are useful for detecting ocular and systemic diseases. Unfortunately, existing tear film sampling methods (Schirmer strip; SS and microcapillary tube; MCT) have significant drawbacks, such as pain, risk of injury, sampling difficulty, and proteomic disparities between methods. Here, we present an alternative tear protein sampling method using soft contact lenses (SCLs)
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Neat plasma proteomics: getting the best out of the worst Clin. Proteom. (IF 3.8) Pub Date : 2024-03-12 Ines Metatla, Kevin Roger, Cerina Chhuon, Sara Ceccacci, Manuel Chapelle, Pierre-Olivier Schmit, Vadim Demichev, Ida Chiara Guerrera
Plasma proteomics holds immense potential for clinical research and biomarker discovery, serving as a non-invasive "liquid biopsy" for tissue sampling. Mass spectrometry (MS)-based proteomics, thanks to improvement in speed and robustness, emerges as an ideal technology for exploring the plasma proteome for its unbiased and highly specific protein identification and quantification. Despite its potential
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Proteomics of prostate cancer serum and plasma using low and high throughput approaches Clin. Proteom. (IF 3.8) Pub Date : 2024-03-12 Ghaith M. Hamza, Rekha Raghunathan, Stephanie Ashenden, Bairu Zhang, Eric Miele, Andrew F. Jarnuczak
Despite progress, MS-based proteomics in biofluids, especially blood, faces challenges such as dynamic range and throughput limitations in biomarker and disease studies. In this work, we used cutting-edge proteomics technologies to construct label-based and label-free workflows, capable of quantifying approximately 2,000 proteins in biofluids. With 70µL of blood and a single depletion strategy, we
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Correction to: Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources Clin. Proteom. (IF 3.8) Pub Date : 2024-03-07 Sara R. Savage, Bing Zhang
Correction to: Clinical Proteomics (2023) 17:27 https://doi.org/10.1186/s12014-020-09290-x In the main text, under the section heading “Knowledge bases of kinases and phosphatases“, 6th paragraph, the 3rd sentence that reads as “DEPOD used data from HuPho as a starting point and therefore contains much of the same information [19]” should have read as “DEPOD also includes pathways, substrates, and
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Closing the gaps in patient management of dyslipidemia: stepping into cardiovascular precision diagnostics with apolipoprotein profiling Clin. Proteom. (IF 3.8) Pub Date : 2024-03-01 Esther Reijnders, Arnoud van der Laarse, L. Renee Ruhaak, Christa M. Cobbaert
In persons with dyslipidemia, a high residual risk of cardiovascular disease remains despite lipid lowering therapy. Current cardiovascular risk prediction mainly focuses on low-density lipoprotein cholesterol (LDL-c) levels, neglecting other contributing risk factors. Moreover, the efficacy of LDL-c lowering by statins resulting in reduced cardiovascular risk is only partially effective. Secondly
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Proteomic analysis of plasma proteins from patients with cardiac rupture after acute myocardial infarction using TMT-based quantitative proteomics approach Clin. Proteom. (IF 3.8) Pub Date : 2024-03-01 Jingyuan Hou, Qiaoting Deng, Xiaohong Qiu, Sudong Liu, Youqian Li, Changjing Huang, Xianfang Wang, Qunji Zhang, Xunwei Deng, Zhixiong Zhong, Wei Zhong
Cardiac rupture (CR) is a rare but catastrophic mechanical complication of acute myocardial infarction (AMI) that seriously threatens human health. However, the reliable biomarkers for clinical diagnosis and the underlying signaling pathways insights of CR has yet to be elucidated. In the present study, a quantitative approach with tandem mass tag (TMT) labeling and liquid chromatography–tandem mass
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Proteomic analysis of breast cancer based on immune subtypes Clin. Proteom. (IF 3.8) Pub Date : 2024-02-29 Yeonjin Jeon, GunHee Lee, Hwangkyo Jeong, Gyungyub Gong, JiSun Kim, Kyunggon Kim, Jae Ho Jeong, Hee Jin Lee
Immunotherapy is applied to breast cancer to resolve the limitations of survival gain in existing treatment modalities. With immunotherapy, a tumor can be classified into immune-inflamed, excluded and desert based on the distribution of immune cells. We assessed the clinicopathological features, each subtype’s prognostic value and differentially expressed proteins between immune subtypes. Immune subtyping
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Highly sensitive therapeutic drug monitoring of infliximab in serum by targeted mass spectrometry in comparison to ELISA data Clin. Proteom. (IF 3.8) Pub Date : 2024-02-29 Andreas Hentschel, Gina Piontek, Rob Dahlmann, Peter Findeisen, Roman Sakson, Phil Carbow, Thomas Renné, Yvonne Reinders, Albert Sickmann
Presently, antibody concentration measurements for patients undergoing treatment are predominantly determined by ELISA, which still comes with known disadvantages. Therefore, our aim was to establish a targeted mass-spectrometric assay enabling the reproducible absolute quantification of peptides from the hypervariable and interaction regions of infliximab. Peptides of infliximab were measured post-trypsin
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Proteomic insights into the pathophysiology of hypertension-associated albuminuria: Pilot study in a South African cohort Clin. Proteom. (IF 3.8) Pub Date : 2024-02-24 Melanie A. Govender, Stoyan H. Stoychev, Jean-Tristan Brandenburg, Michèle Ramsay, June Fabian, Ireshyn S. Govender
Hypertension is an important public health priority with a high prevalence in Africa. It is also an independent risk factor for kidney outcomes. We aimed to identify potential proteins and pathways involved in hypertension-associated albuminuria by assessing urinary proteomic profiles in black South African participants with combined hypertension and albuminuria compared to those who have neither condition
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Recent progress in mass spectrometry-based urinary proteomics Clin. Proteom. (IF 3.8) Pub Date : 2024-02-22 Neha Joshi, Kishore Garapati, Vivek Ghose, Richard K. Kandasamy, Akhilesh Pandey
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers.
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Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients Clin. Proteom. (IF 3.8) Pub Date : 2024-02-22 Tomonori Kaneko, Sally Ezra, Rober Abdo, Courtney Voss, Shanshan Zhong, Xuguang Liu, Owen Hovey, Marat Slessarev, Logan Robert Van Nynatten, Mingliang Ye, Douglas Fraser, Shawn Shun-Cheng Li
SARS-CoV-2 infection triggers extensive host immune reactions, leading to severe diseases in certain individuals. However, the molecular basis underlying the excessive yet non-productive immune responses in severe COVID-19 remains incompletely understood. In this study, we conducted a comprehensive analysis of the peripheral blood mononuclear cell (PBMC) proteome and phosphoproteome in sepsis patients
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Lessons learned: establishing a CLIA-equivalent laboratory for targeted mass spectrometry assays – navigating the transition from research to clinical practice Clin. Proteom. (IF 3.8) Pub Date : 2024-02-22 Chia-Li Han, Chi-Ting Lai, Aaron James Reyes, Hao-Chin Yang, Jin-Ying Lu, Shyang-Rong Shih, Kuen-Yuan Chen, Andrew N. Hoofnagle, Sung-Liang Yu, William Bocik, Tara Hiltke, Huan-Chi Chiu, Ching-Yi Wan, Henry Rodriguez, Victoria Zhang, Yu-Ju Chen
Mass spectrometry (MS) assays offer exceptional capabilities in high multiplexity, specificity, and throughput. As proteomics technologies continue advancements to identify new disease biomarkers, transition of these innovations from research settings to clinical applications becomes imperative. To meet the rigorous regulatory standards of clinical laboratories, development of a clinical protein MS
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Comparison of early changes in tear film protein profiles after small incision lenticule extraction (SMILE) and femtosecond LASIK (FS-LASIK) surgery Clin. Proteom. (IF 3.8) Pub Date : 2024-02-17 Petri Mäkinen, Janika Nättinen, Ulla Aapola, Juhani Pietilä, Hannu Uusitalo
Small incision lenticule extraction (SMILE) and femtosecond laser-assisted in situ keratomileusis (LASIK) are widely used surgical methods to correct myopia with comparable efficacy, predictability, and safety. We examined and compared the early changes of tear protein profiles after SMILE and FS-LASIK surgery in order to find possible differences in the initial corneal healing process. SMILE operations
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Exploring the novel duo of Reticulocalbin, and Sideroflexin as future biomarker candidates for Exacerbated Chronic Obstructive Pulmonary Disease Clin. Proteom. (IF 3.8) Pub Date : 2024-02-14 Sonu Das, Supriya Adiody, Jinsu Varghese, M Vanditha, Evelyn Maria, Mathew John
COPD is a complex respiratory disorder with high morbidity and mortality rates. Even with the current conventional diagnostic methods, including circulating inflammatory biomarkers, underdiagnosis rates in COPD remain as high as 70%. Our study was a comparative cross-sectional study that aimed to address the diagnostic challenges by identifying future biomarker candidates in COPD variants. This study
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Correction: Glial cell proteome using targeted quantitative methods for potential multi-diagnostic biomarkers Clin. Proteom. (IF 3.8) Pub Date : 2024-02-10 Narae Kang, Hyun Jeong Oh, Ji Hye Hong, Hyo Eun Moon, Yona Kim, Hyeon-Jeong Lee, Hophil Min, Hyeonji Park, Sang Hun Lee, Sun Ha Paek, Jonghwa Jin
Correction to: Clinical Proteomics (2023) 20:45 https://doi.org/10.1186/s12014-023-09432-x In this article [1] the author name Sun Ha Paek was incorrectly written as Sun Ha Peak. The original article has been corrected. Kang, N., Oh, H.J., Hong, J.H. et al. Glial cell proteome using targeted quantitative methods for potential multi-diagnostic biomarkers. Clin Proteom 20, 45 (2023). https://doi.org/10
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Absolute quantitation of human wild-type DNAI1 protein in lung tissue using a nanoLC-PRM-MS-based targeted proteomics approach coupled with immunoprecipitation Clin. Proteom. (IF 3.8) Pub Date : 2024-02-04 Hui Wang, Xiaoyan Ni, Nicholas Clark, Kristen Randall, Lianne Boeglin, Sudha Chivukula, Caroline Woo, Frank DeRosa, Gang Sun
Dynein axonemal intermediate chain 1 protein (DNAI1) plays an essential role in cilia structure and function, while its mutations lead to primary ciliary dyskinesia (PCD). Accurate quantitation of DNAI1 in lung tissue is crucial for comprehensive understanding of its involvement in PCD, as well as for developing the potential PCD therapies. However, the current protein quantitation method is not sensitive
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Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma Clin. Proteom. (IF 3.8) Pub Date : 2024-01-30 Sara R. Savage, Yuefan Wang, Lijun Chen, Scott Jewell, Chelsea Newton, Yongchao Dou, Qing Kay Li, Oliver F. Bathe, Ana I. Robles, Gilbert S. Omenn, Mathangi Thiagarajan, Hui Zhang, Galen Hostetter, Bing Zhang
Omics characterization of pancreatic adenocarcinoma tissue is complicated by the highly heterogeneous and mixed populations of cells. We evaluate the feasibility and potential benefit of using a coring method to enrich specific regions from bulk tissue and then perform proteogenomic analyses. We used the Biopsy Trifecta Extraction (BioTExt) technique to isolate cores of epithelial-enriched and stroma-enriched
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Recent developments in mass-spectrometry-based targeted proteomics of clinical cancer biomarkers Clin. Proteom. (IF 3.8) Pub Date : 2024-01-30 Deborah Wenk, Charlotte Zuo, Thomas Kislinger, Lusia Sepiashvili
Routine measurement of cancer biomarkers is performed for early detection, risk classification, and treatment monitoring, among other applications, and has substantially contributed to better clinical outcomes for patients. However, there remains an unmet need for clinically validated assays of cancer protein biomarkers. Protein tumor markers are of particular interest since proteins carry out the
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An LC–MS-based designated comparison method with similar performance to the Lp(a) reference measurement procedure to guide molar Lp(a) standardization Clin. Proteom. (IF 3.8) Pub Date : 2024-01-24 Nina M. Diederiks, L. Renee Ruhaak, Fred P. H. T. M. Romijn, Mervin M. Pieterse, Nico P. M. Smit, Christa M. Cobbaert
The 2022 consensus statement of the European Atherosclerosis Society (EAS) on lipoprotein(a) (Lp(a)) recognizes the role of Lp(a) as a relevant genetically determined risk factor and recommends its measurement at least once in an individual’s lifetime. It also strongly urges that Lp(a) test results are expressed as apolipoprotein (a) (apo(a)) amount of substance in molar units and no longer in confounded
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Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling Clin. Proteom. (IF 3.8) Pub Date : 2024-01-22 Allison L. Hunt, Nicholas W. Bateman, Waleed Barakat, Sasha C. Makohon-Moore, Tamara Abulez, Jordan A. Driscoll, Joshua P. Schaaf, Brian L. Hood, Kelly A. Conrads, Ming Zhou, Valerie Calvert, Mariaelena Pierobon, Jeremy Loffredo, Katlin N. Wilson, Tracy J. Litzi, Pang-Ning Teng, Julie Oliver, Dave Mitchell, Glenn Gist, Christine Rojas, Brian Blanton, Kathleen M. Darcy, Uma N. M. Rao, Emanuel F. Petricoin
Although uterine serous carcinoma (USC) represents a small proportion of all uterine cancer cases, patients with this aggressive subtype typically have high rates of chemotherapy resistance and disease recurrence that collectively result in a disproportionately high death rate. The goal of this study was to provide a deeper view of the tumor microenvironment of this poorly characterized uterine cancer
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Kinase inhibitor pulldown assay (KiP) for clinical proteomics Clin. Proteom. (IF 3.8) Pub Date : 2024-01-16 Alexander B. Saltzman, Doug W. Chan, Matthew V. Holt, Junkai Wang, Eric J. Jaehnig, Meenakshi Anurag, Purba Singh, Anna Malovannaya, Beom-Jun Kim, Matthew J. Ellis
Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based
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Prognostic biomarker discovery based on proteome landscape of Chinese lung adenocarcinoma Clin. Proteom. (IF 3.8) Pub Date : 2024-01-05 Yuqi Huang, Sheng Ma, Jun-Yu Xu, Kun Qian, Yaru Wang, Yi Zhang, Minjia Tan, Ting Xiao
Despite recent innovations in imaging and genomic screening promotes advance in diagnosis and treatment of lung adenocarcinoma (LUAD), there remains high mortality of LUAD and insufficient understanding of LUAD biology. Our previous study performed an integrative multi-omic analysis of LUAD, filling the gap between genomic alterations and their biological proteome effects. However, more detailed molecular
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Quantification of putative ovarian cancer serum protein biomarkers using a multiplexed targeted mass spectrometry assay Clin. Proteom. (IF 3.8) Pub Date : 2024-01-03 Joohyun Ryu, Kristin L. M. Boylan, Carly A. I. Twigg, Richard Evans, Amy P. N. Skubitz, Stefani N. Thomas
Ovarian cancer is the most lethal gynecologic malignancy in women, and high-grade serous ovarian cancer (HGSOC) is the most common subtype. Currently, no clinical test has been approved by the FDA to screen the general population for ovarian cancer. This underscores the critical need for the development of a robust methodology combined with novel technology to detect diagnostic biomarkers for HGSOC
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sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides Clin. Proteom. (IF 3.8) Pub Date : 2023-12-05 Kishore Garapati, Husheng Ding, M. Cristine Charlesworth, Yohan Kim, Roman Zenka, Mayank Saraswat, Dong-Gi Mun, Sandip Chavan, Ashish Shingade, Fabrice Lucien, Jun Zhong, Richard K. Kandasamy, Akhilesh Pandey
Cell surface proteins perform critical functions related to immune response, signal transduction, cell–cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite several enrichment methods
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Quantitative proteomics analysis based on data-independent acquisition reveals the effect of Shenling Baizhu powder (SLP) on protein expression in MAFLD rat liver tissue Clin. Proteom. (IF 3.8) Pub Date : 2023-12-01 Sufei Song, Jixian Zheng, Dongmei Zhao, Anni Zheng, Ye Zhu, Qiuling Xu, Tao Liu
Metabolic associated fatty liver disease (MAFLD) has become the most common chronic liver disease worldwide, and it is also a high-risk factor for the development of other metabolic diseases. Shenling Baizhu powder (SLP) is a traditional Chinese herbal formula with good clinical efficacy against MAFLD. However, its molecular mechanism for the treatment of MAFLD is still not fully understood. This study
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Proteomic analysis of chromophobe renal cell carcinoma and benign renal oncocytoma biopsies reveals shared metabolic dysregulation Clin. Proteom. (IF 3.8) Pub Date : 2023-11-28 Luis B. Carvalho, Susana Jorge, Hugo López-Fernández, Carlos Lodeiro, Rajiv Dhir, Luis Campos Pinheiro, Mariana Medeiros, Hugo M. Santos, José L. Capelo
This study investigates the proteomic landscapes of chromophobe renal cell carcinoma (chRCC) and renal oncocytomas (RO), two subtypes of renal cell carcinoma that together account for approximately 10% of all renal tumors. Despite their histological similarities and shared origins, chRCC is a malignant tumor necessitating aggressive intervention, while RO, a benign growth, is often subject to overtreatment
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Validation of the novel GLAS algorithm as an aid in the detection of liver fibrosis and cirrhosis based on GP73, LG2m, age, and sex Clin. Proteom. (IF 3.8) Pub Date : 2023-11-28 Philip M. Hemken, Xuzhen Qin, Lori J. Sokoll, Laurel Jackson, Fan Feng, Peng Li, Susan H. Gawel, Bailin Tu, Zhihong Lin, James Hartnett, David Hawksworth, Bryan C. Tieman, Toru Yoshimura, Hideki Kinukawa, Shaohua Ning, Enfu Liu, Fanju Meng, Fei Chen, Juru Miao, Xuan Mi, Xin Tong, Daniel W. Chan, Gerard J. Davis
Diagnosis of liver disease at earlier stages can improve outcomes and reduce the risk of progression to malignancy. Liver biopsy is the gold standard for diagnosis of liver disease, but is invasive and sample acquisition errors are common. Serum biomarkers for liver function and fibrosis, combined with patient factors, may allow for noninvasive detection of liver disease. In this pilot study, we tested
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Development of a predictive model to distinguish prostate cancer from benign prostatic hyperplasia by integrating serum glycoproteomics and clinical variables Clin. Proteom. (IF 3.8) Pub Date : 2023-11-21 Caterina Gabriele, Federica Aracri, Licia Elvira Prestagiacomo, Maria Antonietta Rota, Stefano Alba, Giuseppe Tradigo, Pietro Hiram Guzzi, Giovanni Cuda, Rocco Damiano, Pierangelo Veltri, Marco Gaspari
Prostate Cancer (PCa) represents the second leading cause of cancer-related death in men. Prostate-specific antigen (PSA) serum testing, currently used for PCa screening, lacks the necessary sensitivity and specificity. New non-invasive diagnostic tools able to discriminate tumoral from benign conditions and aggressive (AG-PCa) from indolent forms of PCa (NAG-PCa) are required to avoid unnecessary
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Comparison of in-gel and in-solution proteolysis in the proteome profiling of organ perfusion solutions Clin. Proteom. (IF 3.8) Pub Date : 2023-11-15 Corinna M. Snashall, Chris W. Sutton, Letizia Lo Faro, Carlo Ceresa, Rutger Ploeg, Sadr ul Shaheed
The organ perfusion solution (perfusate), collected at clinically and temporally significant stages of the organ preservation and transplantation process, provides a valuable insight into the biological status of an organ over time and prior to reperfusion (transplantation) in the recipient. The objective of this study was to assess two bottom-up proteomics workflows for the extraction of tryptic peptides
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A pathway activity-based proteomic classifier stratifies prostate tumors into two subtypes Clin. Proteom. (IF 3.8) Pub Date : 2023-11-11 Rui Sun, Lingling Tan, Xuan Ding, Jun A, Zhangzhi Xue, Xue Cai, Sainan Li, Tiannan Guo
Prostate cancer (PCa) is the second most common cancer in males worldwide. The risk stratification of PCa is mainly based on morphological examination. Here we analyzed the proteome of 667 tumor samples from 487 Chinese PCa patients and characterized 9576 protein groups by PulseDIA mass spectrometry. Then we developed a pathway activity-based classifier concerning 13 proteins from seven pathways, and
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Candidate biomarkers for treatment benefit from sunitinib in patients with advanced renal cell carcinoma using mass spectrometry-based (phospho)proteomics Clin. Proteom. (IF 3.8) Pub Date : 2023-11-08 Hanneke van der Wijngaart, Robin Beekhof, Jaco C. Knol, Alex A. Henneman, Richard de Goeij-de Haas, Sander R. Piersma, Thang V. Pham, Connie R. Jimenez, Henk M. W. Verheul, Mariette Labots
The tyrosine kinase inhibitor sunitinib is an effective first-line treatment for patients with advanced renal cell carcinoma (RCC). Hypothesizing that a functional read-out by mass spectrometry-based (phospho, p-)proteomics will identify predictive biomarkers for treatment outcome of sunitinib, tumor tissues of 26 RCC patients were analyzed. Eight patients had primary resistant (RES) and 18 sensitive
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Change of histone H3 lysine 14 acetylation stoichiometry in human monocyte derived macrophages as determined by MS-based absolute targeted quantitative proteomic approach: HIV infection and methamphetamine exposure Clin. Proteom. (IF 3.8) Pub Date : 2023-10-25 Katarzyna Macur, Andrew Schissel, Fang Yu, Shulei Lei, Brenda Morsey, Howard S. Fox, Pawel Ciborowski
Histones posttranslational modification represent an epigenetic mechanism that regulate gene expression and other cellular processes. Quantitative mass spectrometry used for the absolute quantification of such modifications provides further insight into cellular responses to extracellular insults such as infections or toxins. Methamphetamine (Meth), a drug of abuse, is affecting the overall function
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Mass spectrometry quantifies target engagement for a KRASG12C inhibitor in FFPE tumor tissue Clin. Proteom. (IF 3.8) Pub Date : 2023-10-25 Andrew G. Chambers, David C. Chain, Steve M. Sweet, Zifeng Song, Philip L. Martin, Matthew J. Ellis, Claire Rooney, Yeoun Jin Kim
Quantification of drug-target binding is critical for confirming that drugs reach their intended protein targets, understanding the mechanism of action, and interpreting dose-response relationships. For covalent inhibitors, target engagement can be inferred by free target levels before and after treatment. Targeted mass spectrometry assays offer precise protein quantification in complex biological
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Comment on “Cerebrospinal fluid camk2a levels at baseline predict long-term progression in multiple sclerosis. Clinical Proteomics” Clin. Proteom. (IF 3.8) Pub Date : 2023-10-25 Fereshteh Behdarvand Dehkordi, Mohammad Chehelgerdi
Dear Editor, I am writing to provide a comparative analysis of the recently published study titled “Cerebrospinal fluid CAMK2A levels at baseline predict long-term progression in multiple sclerosis” conducted by Sohaei et al. [1]. (Clinical Proteomics. 2023 Dec;20(1):1–2). Given the significant findings of this study, it is crucial to assess its contributions in relation to existing research to offer
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Glial cell proteome using targeted quantitative methods for potential multi-diagnostic biomarkers Clin. Proteom. (IF 3.8) Pub Date : 2023-10-24 Narae Kang, Hyun Jeong Oh, Ji Hye Hong, Hyo Eun Moon, Yona Kim, Hyeon-Jeong Lee, Hophil Min, Hyeonji Park, Sang Hun Lee, Sun Ha Peak, Jonghwa Jin
Glioblastoma is one of the most malignant primary brain cancer. Despite surgical resection with modern technology followed by chemo-radiation therapy with temozolomide, resistance to the treatment and recurrence is common due to its aggressive and infiltrating nature of the tumor with high proliferation index. The median survival time of the patients with glioblastomas is less than 15 months. Till
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Validation of ANG-1 and P-SEL as biomarkers of post-COVID-19 conditions using data from the Biobanque québécoise de la COVID-19 (BQC-19) Clin. Proteom. (IF 3.8) Pub Date : 2023-10-24 Eric Yamga, Antoine Soulé, Alain Piché, Amin Emad, Madeleine Durand, Simon Rousseau
The quest for understanding and managing the long-term effects of COVID-19, often referred to as Long COVID or post-COVID-19 condition (PCC), remains an active research area. Recent findings highlighted angiopoietin-1 (ANG-1) and p-selectin (P-SEL) as potential diagnostic markers, but validation is essential, given the inconsistency in COVID-19 biomarker studies. Leveraging the biobanque québécoise
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Proteomic analyses reveal cystatin c is a promising biomarker for evaluation of systemic lupus erythematosus Clin. Proteom. (IF 3.8) Pub Date : 2023-10-18 He Huang, Yukun Zhang, Lan Gui, Li Zhang, Minglong Cai, Yujun Sheng
Systemic lupus erythematosus (SLE) is an autoimmune disease with multiple organ involvement, especially the kidneys. However, the underlying mechanism remains unclear, and accurate biomarkers are still lacking. This study aimed to identify biomarkers to assess organ damage and disease activity in patients with SLE using quantitative proteomics. Proteomic analysis was performed using mass spectrometry
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Redefining serological diagnostics with immunoaffinity proteomics Clin. Proteom. (IF 3.8) Pub Date : 2023-10-12 Jonathan Walter, Zicki Eludin, Andrei P. Drabovich
Serological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The
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A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors Clin. Proteom. (IF 3.8) Pub Date : 2023-09-29 Ankit Halder, Deeptarup Biswas, Aparna Chauhan, Adrita Saha, Shreeman Auromahima, Deeksha Yadav, Mehar Un Nissa, Gayatri Iyer, Shashwati Parihari, Gautam Sharma, Sridhar Epari, Prakash Shetty, Aliasgar Moiyadi, Graham Roy Ball, Sanjeeva Srivastava
Meningiomas are the most prevalent primary brain tumors. Due to their increasing burden on healthcare, meningiomas have become a pivot of translational research globally. Despite many studies in the field of discovery proteomics, the identification of grade-specific markers for meningioma is still a paradox and requires thorough investigation. The potential of the reported markers in different studies
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Development of an ID-LC–MS/MS method using targeted proteomics for quantifying cardiac troponin I in human serum Clin. Proteom. (IF 3.8) Pub Date : 2023-09-27 Meltem Asicioglu, Merve Oztug, Nevin Gul Karaguler
Cardiac troponin is a complex protein consisting of the three subunits I, T and C located in heart muscle cells. When the heart muscle is damaged, it is released into the blood and can be detected. Cardiac troponin I (cTnI) is considered the most reliable and widely accepted test for detecting and confirming acute myocardial infarction. However, there is no current standardization between the commercial
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Identification of potential molecular targets for the treatment of cluster 1 human pheochromocytoma and paraganglioma via comprehensive proteomic characterization Clin. Proteom. (IF 3.8) Pub Date : 2023-09-25 Ondrej Vit, Pavel Talacko, Zdenek Musil, Igor Hartmann, Karel Pacak, Jiri Petrak
Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors. New drug targets and proteins that would assist sensitive PPGL imagining could improve therapy and quality of life of patients with PPGL, namely those with recurrent or metastatic disease. Using a combined proteomic strategy, we looked for such clinically relevant targets among integral membrane proteins (IMPs) upregulated
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Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism, and immune response Clin. Proteom. (IF 3.8) Pub Date : 2023-09-21 Soumyadeep Sarkar, Emily C. Elliott, Hayden R. Henry, Ivo Díaz Ludovico, John T. Melchior, Ashley Frazer-Abel, Bobbie-Jo Webb-Robertson, W. Sean Davidson, V. Michael Holers, Marian J. Rewers, Thomas O. Metz, Ernesto S. Nakayasu
Type 1 diabetes (T1D) results from an autoimmune attack of the pancreatic β cells that progresses to dysglycemia and symptomatic hyperglycemia. Current biomarkers to track this evolution are limited, with development of islet autoantibodies marking the onset of autoimmunity and metabolic tests used to detect dysglycemia. Therefore, additional biomarkers are needed to better track disease initiation
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Identification and verification of plasma protein biomarkers that accurately identify an ectopic pregnancy Clin. Proteom. (IF 3.8) Pub Date : 2023-09-15 Lynn A. Beer, Xiangfan Yin, Jianyi Ding, Suneeta Senapati, Mary D. Sammel, Kurt T. Barnhart, Qin Liu, David W. Speicher, Aaron R. Goldman
Differentiating between a normal intrauterine pregnancy (IUP) and abnormal conditions including early pregnancy loss (EPL) or ectopic pregnancy (EP) is a major clinical challenge in early pregnancy. Currently, serial β-human chorionic gonadotropin (β-hCG) and progesterone are the most commonly used plasma biomarkers for evaluating pregnancy prognosis when ultrasound is inconclusive. However, neither
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Proteome analysis of CD5-positive diffuse large B cell lymphoma FFPE tissue reveals downregulation of DDX3X, DNAJB1, and B cell receptor signaling pathway proteins including BTK and Immunoglobulins Clin. Proteom. (IF 3.8) Pub Date : 2023-09-13 Takuya Hiratsuka, Shinji Ito, Rika Sakai, Tomoyuki Yokose, Tatsuya Endo, Yataro Daigo, Yohei Miyagi, Tatsuaki Tsuruyama
The molecular pathology of diffuse large B cell lymphoma (DLBCL) has been extensively studied. Among DLBCL subtypes, the prognosis of CD5-positive DLBCL is worse than that of CD5-negative DLBCL, considering the central nervous system relapse and poor response to R-CHOP therapy. However, the molecular mechanisms underlying the tumorigenesis and progression of CD5-positive DLBCL remain unknown. To identify
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New mechanisms and biomarkers of lymph node metastasis in cervical cancer: reflections from plasma proteomics Clin. Proteom. (IF 3.8) Pub Date : 2023-09-09 Sai Han, Xiaoli Liu, Shuang Ju, Wendi Mu, Gulijinaiti Abulikemu, Qianwei Zhen, Jiaqi Yang, Jingjing Zhang, Yi Li, Hongli Liu, Qian Chen, Baoxia Cui, Shuxia Wu, Youzhong Zhang
Lymph node metastasis (LNM) and lymphatic vasculature space infiltration (LVSI) in cervical cancer patients indicate a poor prognosis, but satisfactory methods for diagnosing these phenotypes are lacking. This study aimed to find new effective plasma biomarkers of LNM and LVSI as well as possible mechanisms underlying LNM and LVSI through data-independent acquisition (DIA) proteome sequencing. A total
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Correction to: Proteomic analysis of human synovial fluid reveals potential diagnostic biomarkers for ankylosing spondylitis Clin. Proteom. (IF 3.8) Pub Date : 2023-09-02 Ji-Hyun Lee, Jae Hun Jung, Jeesoo Kim, Won-Ki Baek, Jinseol Rhee, Tae-Hwan Kim, Sang-Hyon Kim, Kwang Pyo Kim, Chang-Nam Son, Jong-Seo Kim
Following publication of the original article [1], the authors noticed the errors in Fig. 4 and Supplementary Fig. 1. In the Fig. 4, the CFHR5 band of G1-10 is duplicated with the C9 band. In the Fig. 4 and Supplementary Fig. 1, the transferrin band of O6-10 is duplicated with the A6-10, independent sample O1-5. In the Fig. 4 and Supplementary Fig. 1, the transferrin band of R6-10 is duplicated with
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Cerebrospinal fluid camk2a levels at baseline predict long-term progression in multiple sclerosis Clin. Proteom. (IF 3.8) Pub Date : 2023-08-29 Dorsa Sohaei, Simon Thebault, Lisa M. Avery, Ihor Batruch, Brian Lam, Wei Xu, Rubah S. Saadeh, Isobel A. Scarisbrick, Eleftherios P. Diamandis, Ioannis Prassas, Mark S. Freedman
Multiple sclerosis (MS) remains a highly unpredictable disease. Many hope that fluid biomarkers may contribute to better stratification of disease, aiding the personalisation of treatment decisions, ultimately improving patient outcomes. The objective of this study was to evaluate the predictive value of CSF brain-specific proteins from early in the disease course of MS on long term clinical outcomes
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Mass spectrometry-based proteomics as an emerging tool in clinical laboratories Clin. Proteom. (IF 3.8) Pub Date : 2023-08-26 Alemayehu Godana Birhanu
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these
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Proteomic analysis of 92 circulating proteins and their effects in cardiometabolic diseases Clin. Proteom. (IF 3.8) Pub Date : 2023-08-07 Corinne Carland, Grace Png, Anders Malarstig, Pik Fang Kho, Stefan Gustafsson, Karl Michaelsson, Lars Lind, Emmanouil Tsafantakis, Maria Karaleftheri, George Dedoussis, Anna Ramisch, Erin Macdonald-Dunlop, Lucija Klaric, Peter K. Joshi, Yan Chen, Hanna M. Björck, Per Eriksson, Julia Carrasco-Zanini, Eleanor Wheeler, Karsten Suhre, Arthur Gilly, Eleftheria Zeggini, Ana Viñuela, Emmanouil T. Dermitzakis
Human plasma contains a wide variety of circulating proteins. These proteins can be important clinical biomarkers in disease and also possible drug targets. Large scale genomics studies of circulating proteins can identify genetic variants that lead to relative protein abundance. We conducted a meta-analysis on genome-wide association studies of autosomal chromosomes in 22,997 individuals of primarily
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Identification of SARS-CoV-2 biomarkers in saliva by transcriptomic and proteomics analysis Clin. Proteom. (IF 3.8) Pub Date : 2023-08-03 Lina M. Marin, George S. Katselis, Paulos Chumala, Stephen Sanche, Lucas Julseth, Erika Penz, Robert Skomro, Walter L. Siqueira
The detection of SARS-CoV-2 biomarkers by real time PCR (rRT-PCR) has shown that the sensitivity of the test is negatively affected by low viral loads and the severity of the disease. This limitation can be overcome by the use of more sensitive approaches such as mass spectrometry (MS), which has not been explored for the detection of SARS-CoV-2 proteins in saliva. Thus, this study aimed at assessing
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Proteomic analysis identifies subgroups of patients with active systemic lupus erythematosus Clin. Proteom. (IF 3.8) Pub Date : 2023-07-29 Kevin Y. C. Su, John A. Reynolds, Rachel Reed, Rachael Da Silva, Janet Kelsall, Ivona Baricevic-Jones, David Lee, Anthony D. Whetton, Nophar Geifman, Neil McHugh, Ian N. Bruce
Systemic lupus erythematosus (SLE) is a clinically and biologically heterogenous autoimmune disease. We aimed to investigate the plasma proteome of patients with active SLE to identify novel subgroups, or endotypes, of patients. Plasma was collected from patients with active SLE who were enrolled in the British Isles Lupus Assessment Group Biologics Registry (BILAG-BR). The plasma proteome was analysed
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Comparative proteomics analysis in different stages of urothelial bladder cancer for identification of potential biomarkers: highlighted role for antioxidant activity Clin. Proteom. (IF 3.8) Pub Date : 2023-07-27 Samira Tabaei, Mohammad Reza Haghshenas, Ali Ariafar, Kambiz Gilany, Allan Stensballe, Shirin Farjadian, Abbas Ghaderi
Non-muscle-invasive bladder cancer (NMIBC) has a high recurrence rate and muscle-invasive bladder cancer (MIBC) has unfavorable outcomes in urothelial bladder cancer (UBC) patients. Complex UBC-related protein biomarkers for outcome prediction may provide a more efficient management approach with an improved clinical outcome. The aim of this study is to recognize tumor-associated proteins, which are
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Associations of circulating proteins with lipoprotein profiles: proteomic analyses from the OmniHeart randomized trial and the Atherosclerosis Risk in Communities (ARIC) Study Clin. Proteom. (IF 3.8) Pub Date : 2023-07-03 Hyunju Kim, Alice H. Lichtenstein, Peter Ganz, Edgar R. Miller, Josef Coresh, Lawrence J. Appel, Casey M. Rebholz
Within healthy dietary patterns, manipulation of the proportion of macronutrient can reduce CVD risk. However, the biological pathways underlying healthy diet-disease associations are poorly understood. Using an untargeted, large-scale proteomic profiling, we aimed to (1) identify proteins mediating the association between healthy dietary patterns varying in the proportion of macronutrient and lipoproteins
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Development of a rapid and specific MALDI-TOF mass spectrometric assay for SARS-CoV-2 detection Clin. Proteom. (IF 3.8) Pub Date : 2023-07-01 Lydia Kollhoff, Marc Kipping, Manfred Rauh, Uta Ceglarek, Günes Barka, Frederik Barka, Andrea Sinz
We have developed a rapid and highly specific assay for detecting and monitoring SARS-CoV-2 infections by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). As MALDI-TOF mass spectrometers are available in a clinical setting, our assay has the potential to serve as alternative to the commonly used reverse transcriptase quantitative polymerase chain reaction
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VCAM-1 complements CA-125 in detecting recurrent ovarian cancer Clin. Proteom. (IF 3.8) Pub Date : 2023-06-25 Jin Song, Lori J. Sokoll, Zhen Zhang, Daniel W. Chan
Close to three-quarters of ovarian cancer cases are frequently diagnosed at an advanced stage, with more than 70% of them failing to respond to primary therapy and relapsing within 5 years. There is an urgent need to identify strategies for early detection of ovarian cancer recurrence, which may lead to earlier intervention and better outcomes. A customized magnetic bead-based 8-plex immunoassay was
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Identification of ORM1, vWF, SPARC, and PPBP as immune-related proteins involved in immune thrombocytopenia by quantitative LC-MS/MS Clin. Proteom. (IF 3.8) Pub Date : 2023-06-24 Dong-mei Yin, Dai Yuan, Rui-jie Sun, Hong-zhi Xu, Shou-yong Hun, Xiao-hui Sui, Ning-ning Shan
Immune thrombocytopenia (ITP) is a common autoimmune disease characterized by loss of immune tolerance to platelet autoantigens leading to excessive destruction and insufficient production of platelets. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) was performed to detect the differentially expressed proteins in bone marrow samples from active ITP patients and normal controls
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Orthogonal proteomics methods warrant the development of Duchenne muscular dystrophy biomarkers Clin. Proteom. (IF 3.8) Pub Date : 2023-06-12 Camilla Johansson, Helian Hunt, Mirko Signorelli, Fredrik Edfors, Andreas Hober, Anne-Sophie Svensson, Hanna Tegel, Björn Forstström, Annemieke Aartsma-Rus, Erik Niks, Pietro Spitali, Mathias Uhlén, Cristina Al-Khalili Szigyarto
Molecular components in blood, such as proteins, are used as biomarkers to detect or predict disease states, guide clinical interventions and aid in the development of therapies. While multiplexing proteomics methods promote discovery of such biomarkers, their translation to clinical use is difficult due to the lack of substantial evidence regarding their reliability as quantifiable indicators of disease
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Tailored therapeutic decision of rheumatoid arthritis using proteomic strategies: how to start and when to stop? Clin. Proteom. (IF 3.8) Pub Date : 2023-06-10 Shuo-Fu Chen, Fu-Chiang Yeh, Ching-Yun Chen, Hui-Yin Chang
Unpredictable treatment responses have been an obstacle for the successful management of rheumatoid arthritis. Although numerous serum proteins have been proposed, there is a lack of integrative survey to compare their relevance in predicting treatment outcomes in rheumatoid arthritis. Also, little is known about their applications in various treatment stages, such as dose modification, drug switching
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Comparative proteomic analysis of glomerular proteins in IgA nephropathy and IgA vasculitis with nephritis Clin. Proteom. (IF 3.8) Pub Date : 2023-05-13 Hajime Kaga, Hirotoshi Matsumura, Ayano Saito, Masaya Saito, Fumito Abe, Takehiro Suzuki, Naoshi Dohmae, Masafumi Odaka, Atsushi Komatsuda, Hideki Wakui, Naoto Takahashi
IgA nephropathy (IgAN) and IgA vasculitis with nephritis (IgAVN) are related glomerular diseases characterized by marked similarities in immunological and histological findings. We herein performed a comparative proteomic analysis of glomerular proteins in IgAN and IgAVN. We used renal biopsy specimens from 6 IgAN patients without nephrotic syndrome (NS) (IgAN-I subgroup), 6 IgAN patients with NS (IgAN-II
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The rapid detection of procalcitonin in septic serum using immunoaffinity MALDI chips Clin. Proteom. (IF 3.8) Pub Date : 2023-05-11 Josef Dvorak, Jana Novakova, Lucie Kraftova, Vendula Studentova, Martin Matejovic, Jaroslav Radej, Thomas Karvunidis, Jan Horak, Marcela Kralovcova, Jaroslav Hrabak, Zuzana Kalaninova, Michael Volny, Petr Novak, Petr Pompach
Sepsis is a common worldwide health condition with high mortality. It is caused by a dysregulated immune response to the pathogen. Severe infections resulting in sepsis can be also determined by monitoring several bloodstream biomarkers, one of them being pro-hormone procalcitonin (PCT). PCT concentration in the bloodstream correlates well with sepsis and in severe cases increases up to a thousand