The ultimate goals of this proposal are to develop broadly applicable tools to analyze glycopeptides in complex matrices and to apply those tools for the analysis of human milk and aggressive breast cancer cells. This work would be accomplished by completing three specific aims: (1) Complete our fully automated glycopeptide analysis tool package, which we started during the first period of this grant's funding (2) Develop the usage of massive inclusion lists to increase the number of glycopeptide ions characterized by MS/MS. (3) Tackle two challenges in glycopeptide analyses that are beyond the reach of today's technology: Project 1) Identify glycopeptide-based biomarkers that are only present in aggressive breast cancer. Project 2) Provide a complete profiling of N- and O-linked glycopeptides in human milk. The bulk of the work would be completed by combining expertise in software design, biological sample handling, HPLC, and mass spectrometry to develop the necessary tools. The utility of the tools would be demonstrated by applying them to complete projects relevant women's health: Specifically, we would provide a more detailed insight into the unique properties of human milk than has ever before been provided, and we would characterize the glycosylation on 10-50 known glycopeptide markers of aggressive breast cancer. In addition to the contributions we make to women's health, this work would drive the field of glycoproteomics forward: The methods for glycoprotein analysis are enabling bioanalytical technologies that can be used in a variety of venues, from protein structure/function analyses to pharmaceutical development, to biomarker discovery and development.