We offer quantitative and qualitative proteomics services using LC-MSn technologies, from the analysis of a single protein or peptide to large scale proteome-wide quantification. Our rates include sample preparation from harvested cell pellets, elutions post-enrichment or purification, or gel bands through data acquisition, quantification, and statistical analysis. Trained users may perform basic sample preparation steps in their own lab and submit processed peptides or proteins for desalting, LCMS, and data analysis by the shared resource.
If the general descriptions of our services do not quite fit your project, come talk to us! Every project is unique and we will work with you to design experiments that fits the needs of your research using the resources we have.
Whole cell proteomics
Quantify changes in protein abundance across a cellular, tissue, or subcellular fraction proteome under different experimental conditions. We currently employ tandem mass tag (TMT) based quantification and can accommodate multiplexing of up to 18 samples.
Whole cell phosphoproteomics
Quantify changes in the phosphoproteome across different experimental conditions. We currently employ tandem mass tag (TMT) based quantification and can accommodate multiplexing of up to 18 samples.
Interactomics
Identify interacting proteins or quantify changes in interactors or PTMs across biological conditions. Common submissions include elutions from immunoprecipitations or tagged pulldowns, such as streptavidin pulldowns from proximity biotinylation experiments.
Secretomics
Identify proteins secreted into cellular supernatant and quantify differential secretion between conditions. We currently employ tandem mass tag (TMT) based quantification and can accommodate multiplexing of up to 18 samples.
Immunopeptidomics
Identify peptides presented by MHCI or II complexes. MHC complexes are immunoprecipitated and bound peptides are extracted using an acidic elution. Peptide sequences are identified by searching raw spectral data against a protein database of the appropriate organism with no proteolytic specificity.
Drug target identification
Identify proteins that bind a drug or small molecule of interest. We recommend the peptide-centric local stability assay (PELSA), but can also support cellular thermal shift assay (CETSA) or proteome integral solubility alteration (PISA) projects. Drug treatments can be carried out in-cell or in-lysate for target identification. We currently employ tandem mass tag (TMT) based quantification and can accommodate multiplexing of up to 18 samples.
Gel band analysis
Identify an unknown protein or degradation product from a gel band.
Protein modifications
Identify and localize protein modifications from a gel band, purified protein, or immunoprecipitation. We can quantify site occupancies with label-free or stable isotope based methods, depending on the modification.
Quality control for protein purifications
Confirm protein identity, assess protein purity post-purification, identify co-purifying proteins.
Intact protein mass
Confirm purified protein/complex is of the expected molecular weight, confirm tag cleavage, quantify covalent compound labeling efficiency. We employ ESI-MS for intact protein analysis.
Targeted peptide or protein quantification
Stable isotope-labeled standards enable determination of molar protein or peptide amount, or quantification of differential levels between conditions.
Crosslinking mass spectrometry
Identify inter- and intra-molecular crosslinked (e.g. BS3, DSSO, SMCC) peptides on purified protein or complex as a compliment to x-ray crystallography or cryo-EM structural studies.
Consultations
We will work with you to determine the most appropriate experimental design and services to meet the needs of your project.
Training
We offer training to shared resource users in basic sample processing, including protein digestions and cleanup of detergent-containing samples (SP3).