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Using AUC of specific XICs that have MS/MS spectra that match spinophilin tryptic peptides phosphorylated at Ser17 and Ser100 (Figures 4(a) and 4(c), respectively), we found that spinophilin phosphorylation at both Ser17 and Ser100 was increased by 6-OHDA lesioning (Figures 4(b) and 4(d); * p [less than or equal to] 0.05).
Caption: Figure 2: Reduced AUC of XICs matching NF-M in spinophilin immunoprecipitates isolated from the synaptic fraction of DA depleted striatum.
 Nonstandard abbreviations: NT-proBNP, N-terminal pro-B-type natriuretic peptide (1-76); BNP, B-type natriuretic peptide (1-32); HF, heart failure; proBNP, pro-B-type natriuretic peptide (1-108); (NT-) proBNP, N-terminal pro-B-type natriuretic peptide (1-76)or proBNP (1-108); mAbs, monoclonal antibodies; IP, immunoprecipitation; pAb, polyclonal antibody; aa, amino acids; TIP, tandem immunoaffinity purification; [mu]-IA-HPLC, [mu]-immunoaffinity-HPLC; BEMAD, [beta]-elimination and Michael addition; nano-LC [ESIMS.sup.n], nano-flow liquid chromatography electrospray ionization multistage mass spectrometry; nano-LC MALDI-TOF MS/MS, nano-flow liquid chromatography MALDITOF tandem mass spectrometry; XICs, extracted ion chromatograms.
XICs around this median retention time are then generated and integrated for each sample in the study using the median retention time [+ or -] 0.5 minutes irrespective of whether the particular peptide was identified in an individual sample.
In this method, data-dependent MS2 spectra provide identification of peptides while the peak height or area of the extracted ion chromatogram (XIC) of the MS1 for the peptide parent ion provides quantitative information.
After automatic integration of the data sets, we manually inspected the data (prealgorithm) to record any global aspects of the XICs or integration that might lead to incorrect quantification and added this information as a separate field or "note" in MultiQuant or Skyline, respectively.
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