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Mass spectrometry techniques for detection of COVID-19 viral and host proteins using naso-oropharyngeal swab and plasma
Published in Sanjeeva Srivastava, Multi-Pronged Omics Technologies to Understand COVID-19, 2022
Recently, quantitative discovery proteomics has been widely explored to detect the viral and host peptides from the COVID-19-infected samples (Park et al. 2020; Nikolaev et al. 2020; Demichev et al. 2020). Currently, there are two methods of quantification for MS-based proteomics, label-free (LFQ) and label-based quantification techniques (Bantscheff et al. 2007) (Figure 3.2). In the LFQ approach, the peptides are quantified on the basis of peak intensity and spectral counting measurements. The measurement of intensity occurs at the MS1 level and the quantification of the area under the curve generated from the chromatogram (Latosinska et al. 2015). The quantification using label-based approach is based on the use of stable isotopes such as isotope-coded affinity tag, isobaric tag for relative and absolute quantification (iTRAQ), and tandem mass tag (TMT), a chemical labeling technique (Trinh et al. 2013). The label-based methods allow for the labeling as well as quantification of multiple samples. The combining of multiple samples for one run not only saves the instrument time but also allows for reduced analytical variability. A few research studies have used TMT-based chemical labeling techniques to detect host proteins using COVID-19-infected plasma samples (Shen et al. 2020; Shu et al. 2020).
Emerging Biomedical Analysis
Published in Lawrence S. Chan, William C. Tang, Engineering-Medicine, 2019
DDA and DIA acquisitions are widely used in bottom-up proteomics for both qualitative and quantitative purposes. Peptides are identified by comparing the experimental tandem mass spectra with theoretical tandem mass spectra generated from in silico fragmentation or a spectral library collected in previous experiments. Without any derivatizations, proteins can be quantitatively compared using precursor ion intensities, peak areas, spectral counts or the transition ion intensities (SRM/MRM only) of peptides. Several labeling techniques including stable isotopic labeling of amino acids in cell culture (SILAC), 18O, demethylation, isobaric tags for relative and absolute quantitation (iTRAQ) and tandem mass tags (TMT) are also available for relative and absolute quantitative analysis of peptides and proteins (Zhang et al. 2013).
Loss of thermotolerance in antibiotic-resistant Acinetobacter baumannii
Published in International Journal of Environmental Health Research, 2021
Svjetlana Dekić Rozman, Ana Butorac, Rea Bertoša, Jasna Hrenović, Marina Markeš
Protein digestion and tandem mass tag (TMT) labeling was performed using Thermo Scientific 2-plex Isobaric Label Reagent Set according to the manufacturer’s instructions (Thermo Fisher Scientific, Rockford, USA). The quantitative proteomics experiment was performed independently of the three biological replicates of A. baumannii grown at 36°C and 44°C and A. baumannii grown with the addition of carbapenems at 36°C and 44°C.