In the protein function prediction task, we are given a dataset\{\mathscr{D}=(\textbf{x}_i, \textbf{y}_i)\mid i=1,\ldots ,m\}. For each data sample, there aren_dfeature vectors, called the views,\textbf{x}_{i}^{\left( d\right) }\mid \textbf{x}_{i}^{\left( d\right...
These "signature peptides" function as analytical surrogates. Mass spectrometric analysis of the proteolyzed mixture permits identification of a protein in a complex sample without purifying the protein or obtaining its composite peptide signature.Fred Regnier...
The PCA was carried out using the prcomp R package: data were preliminarily centered and scaled to get zero-mean and unit variance on each protein. Data were analyzed with the SPSS statistical package (version 24.0) and with GraphPad Prism (version 8.0, GraphPad Software). Heat map ...
Finally, each function is accurately predicted by the classifier module based on the representation vectors. Fig. 1 The framework of TPpred-LE Full size image We use the multi-label metrics ACCexample (example-based Accuracy) and F1label (label-based F1-score) to evaluate the overall ...
A Bayesian information criterion was used that added a penalty to each additional fitted peak to reduce over fitting (40). When a protein did not have two adjacent nonzero fractions, the fraction with the highest intensity was used as the peak, and raw intensity values were retained for all...
For each pixel, a Pearson correlation coefficient (ρ) is calculated by the “corr” built-in function of MATLAB. Optimum defocusing range is determined by running the DSC image generation algorithm for different defocusing ranges and maximizing the average SNR for detected particles (Fig. S7). ...
Differential analysis was performed to identify proteins by repeatability test. 2.5. Protein annotation Using eggnog-mapper software (v2.0) to perform Gene Ontology (GO) annotation analysis of the DEPs. The software extracted the GO ID of each protein annotation result and classified the proteins ...
After MS/MS fragmentation, each TMTpro tag generates a unique reporter mass (i.e., TMTpro 126-134Da) in the low-mass region of the high-resolution MS/MS spectrum that is used for relative quantitation of protein expression levels. TMTpro Zero Label Reagent is a “light” version of the...
The concept of PseAAC was first proposed by Chou [29] which is an improvement version of the traditional Amino Acid Composition (AAC). Given a protein sequence P with L amino acid residues:(1)P=R1R2R3−−−−RL AAC will be the 20 dimensionals array, where each element of the ar...
Label properties can refer to the characteristics of a label, such as its size, color, content, and placement. What is label value? "Label value" can refer to the value assigned to a label in various contexts. For example, in a machine learning dataset, each instance's label value is ...