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The Precision Medicine Approach in Oncology
Published in David E. Thurston, Ilona Pysz, Chemistry and Pharmacology of Anticancer Drugs, 2021
MALDI-MSI (Matrix-Assisted Laser Desorption Ionization MS Imaging) and LCM-MS (Laser Capture Microdissection MS) are two new MS-based technologies that are being developed for use in the proteomics area. These techniques, which are still experimental, attempt to use mass spectrometry to image proteins and peptides in cells and tissues. Gel-free isotopic labeling methods such as SILAC (Stable Isotope Labeling with Amino Acids in Cell Culture), iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) and I-TMTs (Isobaric Tandem Mass Tags) are currently capable of quantifying up to thousands of proteins in a single analysis with high reproducibility.
Omics and perinatal medicinePreeclampsia
Published in Moshe Hod, Vincenzo Berghella, Mary E. D'Alton, Gian Carlo Di Renzo, Eduard Gratacós, Vassilios Fanos, New Technologies and Perinatal Medicine, 2019
Piya Chaemsaithong, Liona C. Poon
One study used isobaric tag for relative and absolute quantitation (iTRAQ) analysis of maternal plasma samples taken at 12 weeks of gestation. iTRAQ is a relatively new quantitative proteomics technique applicable to bottom-up mass spectrometry (157–159). Advantages of this technique are that a protein can be identified and quantified from data of multiple peptides often with multiple values per distinct peptide, thereby enhancing confidence in both identity and abundance. In addition, several samples can be combined and analyzed together. The authors found that there were 31 upregulated proteins and 20 downregulated proteins in patients who subsequently developed PE (n = 5), demonstrating the potential for the development of a first trimester screening model for PE using proteomics (160).
Proteomics Approaches to Uncover the Drug Resistance Mechanisms of Microbial Biofilms
Published in Chaminda Jayampath Seneviratne, Microbial Biofilms, 2017
Chaminda Jayampath Seneviratne, Tanujaa Suriyanarayanan, Lin Qingsong, Juan Antonio Vizcaíno
MS-based proteomics analysis can be either qualitative or quantitative. Quantitative MS-based analysis of proteins in samples can be carried out using two main approaches. Differentially expressed proteins can be quantified by either isotopic-labelling or label-free MS analysis. Differential isotopic labelling methods such as isobaric Tags for Relative and Absolute Quantitation (iTRAQ), Isotope-Coded Affinity Tags (ICAT), Stable-Isotope Labelling by Amino acids in Cell culture (SILAC) and Tandem Mass Tag (TMT), among others, can be used for relative quantification, including those studies related to biofilm proteomics [15,77,110,111].
MicroRNA-29a May Influence Myopia Development by Regulating Collagen I
Published in Current Eye Research, 2022
Yi Zhu, Yingjie Zhang, Run Jiang, Keke Zhao, Jibo Zhou
Following transfection with miR-29a mimic inhibitor for 72 h, total protein of SF cells was harvested for proteomic analyses. Proteins were digested into peptides with trypsin using the filter-aided sample preparation method. For each sample, 100 μg of peptide was labeled according to the instructions of the iTRAQ labeling kit (AB Sciex, Framingham, MA, USA). Isobaric tags for relative and absolute quantitation of iTRAQ-labeled peptides were fractionated by strong cation exchange chromatography using the AKTA Purifier 100 system (GE Healthcare, Uppsala, Sweden). The collected fractions were desalted and concentrated by vacuum centrifugation. Each fraction was separated by nano-liquid chromatography followed by tandem mass spectrometry analysis. Protein identification was supported by at least one unique peptide. For protein quantization, a protein was required to produce at least two unique spectra. Quantitative protein ratios were weighted and normalized using the median ratio in MASCOT. Proteins were deemed to be differentially expressed using one-way analysis of variance. Proteins with p < .05 and a fold change of ± 1.2 or greater were considered to be differentially expressed.
How can proteomics overhaul our understanding of Leishmania biology?
Published in Expert Review of Proteomics, 2020
Paul W. Denny, Karunakaran Kalesh
The use of synthetic chemical probes in combination with proteomic MS, known as chemical proteomics, has emerged as a powerful approach for unraveling protein function in various biological systems. Chemical proteomics workflows typically rely on a suitable quantitative proteomic method such as SILAC, iTRAQ (isobaric tags for relative and absolute quantitation) or TMT (tandem mass tag) labeling or LFQ (label-free quantification) for quantitative comparison of the different conditions of the study. Chemical proteomics in Leishmania spp., although in its infancy, has showed glimpses of its unique capabilities. For instance, in a seminal study, Wyllie et al. employed SILAC-based chemical proteomics to identify a set of L. donovani cyclin-dependent kinases (CDKs) as molecular targets of their antileishmanial preclinical candidate compound [21]. Another noteworthy study involves global profiling of substrates of L. donovani N-myristoyltransferase (NMT) using metabolic incorporation with a clickable myristic acid analog and LFQ proteomic MS [22]. With further development in the chemical probing of specific Leishmania proteins, the field of chemical proteomics could significantly contribute to increasing our understanding of the parasite’s biology.
Screening of serum biomarkers of preeclampsia by proteomics combination with bioinformatics
Published in Hypertension in Pregnancy, 2019
Yuee Ling, Jie Su, Jie Lin, Sumei Wang
Since the placenta can only be obtained after delivery, it is not feasible to rely on placental markers for the early diagnosis of preeclampsia. The maternal serum proteins have been proposed as an alternative source to identify novel predictive and diagnostic markers. Isobaric tags for relative and absolute quantitation (iTRAQ) is an effective, high throughput proteomics technique with higher sensitivity, accuracy, and reproducibility, when compared with the traditional methods like two-dimensional gel electrophoresis (2DE) and protein microarray (7). It has been extensively used to screen for disease markers and explore novel drug targets (8,9). Since iTRAQ is also non-invasive and does not require large sample quantities, it is especially suitable for analyzing sera from pregnant women. To this end, we identified the differential expressed serum proteins in PE patients relative to healthy pregnant women using the iTRAQ technology, in order to identify novel markers for PE.