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General Limitations MS proteomics is a powerful tool for the analysis of protein samples, but there are some limits to the techniques we employ in the Proteomics Core. Knowing the limitations of the services we provide can help to ensure your experiment is a success, and you do not incur costs for un…

Computing and Data Analysis Continuous improvement in mass-spectrometry instrumentation means that proteomics facilities are generating a growing amount of data, and tackling increasingly complex datasets. The rise of quantitative proteomics in particular demands robust data analysis techniques to en…

Complex Mixture ID Introduction Modern LC-MS/MS platforms can identify several thousands of proteins from a single sample. We realize that many different types of samples can be submitted for proteomics analsyis, so we accept a wide range of sample formats, including: On-bead (magnetic beads preferre…

Co-IP Experiments Introduction One of the most common types of experiment submitted for analysis in the Proteomics Core is the Co-IP experiment. An antibody against endogenous or tagged protein is used to pull down a protein of interest. The goal of the experiment is to see what comes down with that …

Cutting Gels Introduction Many proteomics samples are well suited for SDS-PAGE, including protein identification and PTM identification. We recognize that a gel approach may not be compatible with all samples, so please contact us if you have concerns about running your sample into a gel. We require …

Intact Mass What do we use to measure the mass of intact proteins? We do LC/MS analysis of intact proteins using a Q-TOF mass spectrometer with electrospray ionization. This means that samples must be free of detergents. An ideal solvent is 5% acetonitrile in water containing 1-5% formic acid or acet…

Gel Band ID Introduction Identification of proteins from visible bands excised from Coomassie or silver-stained gels using mass-spectrometry is generally very successful. Almost all visible Coomassie bands contain enough protein for MS identification. Most silver-stain bands can be identified on our …

Special Stains The Histo Pathology Core offers a wide menu of special stains for improving visualization of normal and disease state chemical moieties. Special Stains that the Core performs on a routine schedule include Oil Red-O stain for neutral lipids, Masson's Trichrome stain for collagen/fibrosi…

Mate-Paired Samples are run on a 1.2% agarose gel and their concentrations quantified by fluorometry. Four µg of genomic DNA are processed using the Nextera Mate Pair Sample Preparation Kit from Illumina. Specifically, the Gel-Plus pathway is followed. Samples are first tagmented then subjected to st…

ChIP-Seq Libraries from 5–10 ng ChIP DNA are prepared using KAPA HTP Library Preparation Kit. The ChIP DNA is quantified on the Qubit® 2.0 Fluorometer from Invitrogen Samples are end repaired, 3' ends adenylated and barcoded with mµltiplex adapters. PCR amplified libraries are purified with Ampure XP…