Over the past decade, a series of experimental strategies for mass spectrometry based
quantitative proteomics and corresponding computational methodology for the processing of …

Mass spectrometry (MS)–based high-throughput proteomics is the core technique for large-
scale protein characterization. Due to the extreme complexity of proteomes, sophisticated …

Missing values weaken the power of label-free quantitative proteomic experiments to
uncover true quantitative differences between biological samples or experimental …

The systematic and quantitative molecular analysis of mutant organisms that has been
pioneered by studies on mutant metabolomes and transcriptomes holds great promise for …

Motivation The proteomics field requires the production and publication of reliable mass
spectrometry-based identification and quantification results. Although many tools or …

It was inevitable that as soon as mass spectrometrists were able to tell biologists which
proteins were in their samples, the next question would be how much of these proteins were …

In a recent study, in vivo metabolic labeling using 15 N traced the rate of label incorporation
among more than 1700 proteins simultaneously and enabled the determination of individual …

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 …

In this study, we present a fully automated tool, called IDEAL-Q, for label-free quantitation
analysis. It accepts raw data in the standard mzXML format as well as search results from …

Detecting differentially expressed proteins is a key goal of proteomics. We describe a label-
free method, the spectral index, for analyzing relative protein abundance in large-scale data …