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Proteomics Services

*Quantitation

The analyses described above are quantitative. Quantitation of peptides/proteins is typically performed to compare a sample to a control (e.g. post-drug treatment, post-knockdown, etc.). Please contact the MAP Core staff to discuss experimental design.

Types of quantitation include:

  1. Isobaric tagging (TMT). The facility provides the labels and will perform the labeling step – up to 18 samples can be multiplexed.
  2. Label-free Data Dependent Acquisition (DDA) using area under the curve or spectral counting. Each sample is analyzed individually. No additional sample preparation required.
  3. Label-free Data Independent Acquisition (DIA) using peak areas in a library-based or Direct-DIA approach. Each sample is analyzed individually. No additional sample preparation required.
  4. Absolute quantitation using heavy labeled peptides for targeted analysis of specific peptides/proteins *only for targeted analyses (see above).

Proteins are typically digested with trypsin then analyzed by LC-MS/MS. Peptide/proteins are identified and quantified using Spectronaut (Label-free DIA), Proteome Discoverer (TMT, label-free DDA), MaxQuant (label-free DDA, APMS projects only), or FragPipe (label-free DDA). Further data analysis is conducted in Perseus, and/or R. The MAP Core can provide publication quality figures such as bar graphs, volcano plots, PCA plots, hierarchical clustering with heat maps, pathway enrichment plots, as well as perform bioinformatics analyses using DAVID or IPA, among other programs.