IDEAL-Q

[…] to estimate how close our hipsc cell lines to hesc cell lines at protein expression level (fig. ); the hipsc cell lines were expected to be very similar to the hesc cell lines. since the output of ideal-q, the software we used to quantify proteins, is not absolute expression level but relative expression ratio, we can only compare protein profiles using ratios with respect to the same base […]

[…] respectively. all ms raw data were processed with proteome discover version 2.1 (thermo fisher scientific). for label-free quantification of palmitoylated peptides, data analysis was performed using ideal-q software [34]. membrane proteomic quantitation was performed by proteome discover version 2.1. full experimental procedures are available in the supplementary data., for subcellular […]

[…] partner repository with the dataset identifier pxd000375 and doi 10.6019/pxd000375., the quantitation of phosphoproteomics and proteomics were performed by the semi label free algorithm by using ideal-q software. firstly, readw (xcalibur, thermo finnigan) program was used to convert the raw data files acquired from the ltq-orbitrap into mzxml file format for peptide peak reconstruction. […]

[…] identification, raw data files from ms/ms data were converted into peak lists using mascot distiller (matrix science; version 2.3.2) using the default parameters. for protein quantification, we used ideal-q software (version 1.0.1.1) to analyze the lc-ms/ms data., total rna was extracted from each mouse liver using trizol and an rneasy mini kit (qiagen), by following the manufacturer’s […]

[…] peak around the mean value, at the same time having heavy tails due to blunders. the q–q plots indicate a normal distribution including blunders which lead to a deviation from the linear shape of an ideal q–q plot. the distributions show a tendency towards a negative skew, with large chm differences occurring in the left tail pointing at a crop height underestimation in the chms derived from k2 […]

[…] (condition a) (). the quantitative phosphoproteomic approach used in this study combined our previously developed automatic ph/acid-controlled imac procedure for phosphopeptide enrichment and the ideal-q algorithm for label-free quantification (see workflow in )., a total of 3,752 non-redundant phosphopeptides that mapped to 3,079 unique phosphorylation sites originating from 1,266 proteins […]