EIC is fine for routine analyses where sensitivity is not an issue. It's also possible to simply integrate extracted-ion chromatograms (EIC) from non-targeted LC/MS experiments. The Core has a long-standing focus on quantitative analysis, typically with selected-ion monitoring (SIM) or multiple-reaction monitoring (MRM) for small molecules or targeted peptides, and spectral counting or iTRAQ for proteins. Quantitation: Spectral Counting, iTRAQ, and Multiple Reaction Monitoring We also have a customizable Python routine that can prepare unconventionally-modified proteins for successful Mascot searches. Significant proteins and metabolites can then be subjected to pathway analysis to gain some insight into the biochemistry of the systems both the comparisons and the pathway analyses can be done with Mass Profiler Professional.

targeted MS/MS analysis of the compounds that changed as a result of the experiment. comparison of results between or among various experimental conditions, 3. initial analysis with a high-resolution instrument (ESI-TOF or QTOF) to provide exact masses, 2. Metabolomics experiments often proceed in three stages 1. After analysis with Scaffold, the results can be examined anywhere on a free download of Scaffold Viewer.

Scaffold incorporates and manipulates the results of these searches and provides an efficient way to evaluate the data and provide some statistical analyses. Mascot, Spectrum MIll, and X!Tandem will compare these spectra with theoretical spectra based on known protein sequences and generate lists of potential protein identies. Proteomics experiments typically involve digestion of a protein mixture followed by LC/MS/MS analyses that generate many hundreds of peptide mass spectra often of varying quality. Both commercial and internet freeware packages are available, and the Core uses and advises on both types. Mass spectrometry-based proteomics and metabolomics experiments generate large data sets that can be effectively exploited only with the help of appropriate software. Database Searching, Mining, and Pathway Analysis

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