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Emerging Biomedical Analysis
Published in Lawrence S. Chan, William C. Tang, Engineering-Medicine, 2019
To look into the possibility of identifying protein biomarkers in ovarian cancer patients, another group of investigators targeted urine, the biological sample collected by the most non-invasive method. In this pilot study, urine samples from 20 ovarian cancer patients and 20 patients with benign ovarian diseases were analyzed by MS using label-free quantification. This study found that the levels of 23 different proteins were significantly elevated between the patient sets. Using another method, the levels of several proteins (LYPD1, LYVE1, PTMA, and SCGB1A1) were confirmed to be increased (Sandow et al. 2018). This discovery will pave the way for further investigation into large populations of patients so as to identify the definitive biomarkers for ovarian cancer.
Advances in phosphoproteomics and its application to COPD
Published in Expert Review of Proteomics, 2022
Xiaoyin Zeng, Yanting Lan, Jing Xiao, Longbo Hu, Long Tan, Mengdi Liang, Xufei Wang, Shaohua Lu, Tao Peng, Fei Long
Label-free quantification is more prevalent among researchers than labeled quantification due to the high cost, low labeling efficiency, and limited sample sizes. For example, Bouhaddou et al. [103] used DIA phosphoproteomics to study the panoramic changes in the phosphoproteome of Vero cells infected with SARS-CoV 2, which provides a new strategy for the treatment of neocrown pneumonia. Xu et al. [104] used DDA phosphorylation proteomics to identify 22,564 phosphorylation modification sites in lung adenocarcinoma (LUAD) and combined them with proteomic data analysis to obtain HSP90AB protein as a plasma biomarker for the prognosis of LUAD patients. Li et al. [105] used DIA phosphorylation proteomics to quantify 47,786 phosphorylated sites and successfully distinguished patients with or without metastatic colorectal cancer. Wang and colleagues [3] compared Ti4+-IMAC and CaTiO3 affinity chromatography materials applied to the phosphoproteome in the saliva of lung cancer patients by DDA quantification and found that Ti4+-IMAC identified additional phosphorylated peptides.
Proteogenomic interrogation of cancer cell lines: an overview of the field
Published in Expert Review of Proteomics, 2021
The most straightforward approach to protein quantification by mass spectrometry is through label-free quantification (LFQ). LFQ requires no additional sample preparation for standard LC-MS/MS for protein identification, and proteins are typically quantified using the normalized sum of the total intensity of peptide ions for a given protein. Peptide quantification is primarily performed by either spectral counting or extracted ion chromatogram (XIC) integration: the former counts and sums up the number of spectra assigned to all peptides mapped to a protein, while the latter sums up the area under the chromatogram of peptides mapped to a protein [24]. A number of methods have been devised for protein intensity normalization, including intensity-based absolute quantification (iBAQ), Top3 and MaxLFQ [25]. The main limitation of LFQ is that, due to inter-run variations on LC-MS/MS platforms, it can be difficult to overcome batch effects that often arise when running multiple samples over an extended period, even using the same mass spectrometer. Nevertheless, its ease, cost-effectiveness and speed allow LFQ to be used for a diverse set of experimental conditions, from biomarker discovery to drug screening to studying cancer mechanisms in CCLs [26].
Label-free quantitative proteomics identifies Smarca4 is involved in vascular calcification
Published in Renal Failure, 2019
Chan Wang, Yun Tang, Yanmei Wang, Guisen Li, Li Wang, Yi Li
Proteomics is a scientific approach of analyzing and identifying large-scale proteins based on mass spectrometry (MS). Techniques for determining proteomics have chemical labeling methods, such as iTRAQ [10], ICAT [11], and mTRAQ [12]. However, there are some shortcomings of labeling quantification. For example, labeling reagents are expensive, the number of labeled samples is limited and low abundance peptides are difficult to detect. As an alternative method, label-free quantification (LFQ) can avoid such defects. Label-free quantification proteomics usually has a high analytical depth and dynamic range, giving this method an advantage when large global protein changes between different treatments [13]. In order to find novel potential biomarkers for early prevention and diagnosis of hyperphosphorus-induced VC, we used LFQ combined with LC–MS/MS to detect differential proteins between calcific rat aorta vascular smooth muscle cells (RASMCs) and normal RASMCs.