Birgit Schilling Birgit Schilling, Ph.D., joined the Chemistry Core and Mass Spectrometry Laboratory at the Buck Institute for Research of Aging in Novato, CA in 2000 (director: Dr. Gibson). Research projects include investigations of neurodegenerative diseases, cancer, mitochondrial damage, protein oxidative posttranslational modifications, the role of surface glycoconjugates in bacterial pathogenesis etc., but also mass spectrometric method development. Birgit is interested in oxidative damage of proteins, protein phosphorylation, glycosylation, acetylation, and other posttranslational modifications, as well as differential expression of proteins during disease and aging processes. In recent years Birgit worked extensively in the field of protein quantitation to assess differential protein expression, particularly using multiple reaction monitoring stable isotope dilution mass spectrometry (MRM-SID-MS), and other chemical labeling quantitative workflows (i.e., iTRAQ and SILAC), however she also used label free protein/peptide quantitation approaches to investigate discovery mass spectrometric data sets (based on MS1 intensity).

Platform Independent and Label-free Quantitation of Protein Acetylation and phosphorylation using MS1 Extracted Ion Chromatograms in Skyline

Skyline MS1 Filtering: Despite advances in metabolic and post-metabolic labeling methods for quantitative proteomics, there remains a need for better label-free approaches. This need is particularly true for workflows that incorporate affinity enrichment steps on the peptide level where isobaric chemical labels such as iTRAQ and TMT tags may prove problematic, or where SILAC labeling cannot be readily applied. Skyline is an open source software tool originally designed for multiple reaction monitoring assay development and data analysis. We expanded the capabilities of Skyline to process full-scan mass spectral data (MS1) proteomic experiments so that ion intensity chromatograms of many peptide analytes could be integrated across HPLC MS/MS experiments. Moreover, unlike existing programs, Skyline MS1 Filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. To demonstrate the utility of Skyline MS1 Filtering we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important posttranslational modifications, acetylation and phosphorylation, in peptide-centric affinity workflows using mouse and human models.

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