High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection.

The measurement of small molecule metabolites on a large scale offers the opportunity for a more complete understanding of cellular metabolism. We developed a high-throughput method to quantify primary amine-containing metabolites in the yeast Saccharomyces cerevisiae by the use of capillary electrophoresis in combination with fluorescent derivatization of cell extracts. We measured amino acid levels in the yeast deletion collection, a set of approximately 5000 strains each lacking a single gene, and developed a computational pipeline for data analysis.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM).

Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry.

Data-independent tandem mass spectrometry isolates and fragments all of the molecular species within a given mass-to-charge window, regardless of whether a precursor ion was detected within the window. For shotgun proteomics on complex protein mixtures, data-independent MS/MS offers certain advantages over the traditional data-dependent MS/MS: identification of low-abundance peptides with insignificant precursor peaks, more direct relative quantification, free of biases caused by competing precursors and dynamic exclusion, and faster throughput due to simultaneous fragmentation of multiple peptides. However, data-independent MS/MS, especially on low-resolution ion-trap instruments, strains standard peptide identification programs, because of less precise knowledge of the peptide precursor mass and large numbers of spectra composed of two or more peptides.

Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data.

Label-free relative quantitative proteomics is a powerful tool for the survey of protein level changes between two biological samples. We have developed and applied an algorithm using chromatographic alignment of microLC-MS runs to improve the detection of differences between complex protein mixtures. We demonstrate the performance of our software by finding differences in E.

High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry.

Advances in Fourier transform mass spectrometry have made the acquisition of high-resolution and accurate mass measurements routine on a chromatographic time scale. Here we report an algorithm, Hardklör, for the rapid and robust analysis of high-resolution mass spectra acquired in shotgun proteomics experiments. Our algorithm is demonstrated in the analysis of an Escherichia coli enriched membrane fraction.

Estrogen receptor alpha is a putative substrate for the BRCA1 ubiquitin ligase.

The breast cancer suppressor protein, BRCA1, is a ubiquitin ligase expressed in a wide range of tissues. However, inheritance of a single BRCA1 mutation significantly increases a woman's lifetime chance of developing tissue-specific cancers in the breast and ovaries. Recently, studies have suggested this tissue specificity may be linked to inhibition of estrogen receptor alpha (ERalpha) transcriptional activation by BRCA1.