Currently there are no feasible direct methods to establish protein sequences like that of nucleotide polymers; the only method to directly determine the identity and the quantity of proteins in a mixture in large scale is the mass spectrometer, which can determine peptide sequences based on fragme...
Nsp1, Nsp2 and Nsp3 were quantified across all replicate samples at each time point, and strain and, therefore, the summed intensity of these proteins were used as a normalisation factor for other SARS-CoV-2 proteins. Statistics and reproducibility Statistical analysis was performed in R33. ...
A detailed description of the dataset is provided in the human urinary proteome data analysis subsection. We applied DASEV to this dataset and estimated feature-wise mean of non-BPMVs in the control group, BPMV proportion in the control group, detection limit, and variance. We filtered out ...
It has become apparent that peptide and thus protein abundances, as measured by large scale high-throughput shotgun proteomics experiments, are not normally distributed [17,19]. This may be reflective of the complex nature of the proteome, especially when post-translational modifications are taken i...
In order to have a good representation for the levels of lysotracker from the lysosomal labelling, nine images were taken per well. Fluorescence levels were analysed using the MetaXpress' Transfluor application module for punctate staining (parameter <Cell: Pit integrated intensity >). 2.4. Animal...
To enable normalization of intensity data between samples in terms of MS signal fluctuations and post-digestion sample processing differences, equivalent SIS peptide amounts were added to all samples. Manual inspection of signals for each sample was made to ensure correct peak detection, accurate ...
Spectral counts, the method simply counts the number of MS2 spectra identified for a given protein in different biological samples for protein quantification. MS1 peak intensity, the signal intensity trace of a peptide ion digested from a given protein without peptide fragmentation; MS2 peak intensity...
in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-...
Dose intensity is the dose where 6-MP becomes toxic to the patient before reaching the 100% protocol dose of 75 mg/m2. r and ρ denote Pearson’s and Spearman’s correlation coefficients, respectively. n = 6 samples for each plot. d, Western blotting results for individually-expressed ...
We identified about 30% more quantifiable proteins that were found to be low-abundance proteins, which were initially filtered out by the PLGEM-STN analysis. This newly developed statistical framework provides a reliable abundance measurement of low-abundance proteins in the spectral count-based label...