Services

A cost estimate based on the complexity of the sample preparation, sample number, mass spectrometry analysis time, and data analysis time will be calculated using instrument time and scientist time pricing and will be provided to the investigator. Examples of commonly used methods include:

• Global profiling of known metabolites including, but not limited to amino acids, biogenic amines, glycolytic intermediates, and organic acids.
• Untargeted metabolomics using differential analysis software to statistically determine significant features based on data sets containing known IDs, putative IDs, and unknowns.
• Stable isotope tracing in cell culture or in vivo.
• Targeted and global profiling of specific lipid classes.
• Untargeted lipidomics using differential analysis software to determine statistically significant lipid species that are identified based on MS² product ion spectra.

Metabolomics and lipidomics fee for service is stratified into instrument time and scientist time. Instrument time (samples/hour) is variable depending on the methods required to obtain the requested data. These fees take into account instrument reagents including solvents and columns, solvents for extraction, and consumables. Scientist time includes sample preparation and data analysis. Data analysis time depends on the complexity of the study, sample number, and depth of the analysis. Specialized standards and internal standards are sometimes required and the cost will be charged to the user.

• Instrument time $75/hr 
• Scientist time $125/hr

We request that samples are submitted as homogenized tissue or cells in approved buffers/detergents with total protein concentrations measured prior to sample submission by standard assays (e.g. BCA or Bradford). If this is not possible and we are required to perform the protein extraction, an additional charge will be applied. Common types of analyses include:

• Protein identification 
• Label free quantitation
• TMT Multiplexing
• Post-translational modification (PTM) identification and quantitation (e.g., phosphorylation, acetylation, ubiquitination)
• Targeted proteomics—absolute quantification of peptides using stable isotope labeled peptides
• Gel band identification

Proteomics fee for service is billed as cost per sample depending on the requested analysis. The cost per sample takes into account sample preparation costs, instrument time and basic data analysis for quantified protein samples given to the MSC by the investigator. Protein extraction and quantitation performed by the MSC will cost an additional $100/sample. Request for extended gradients will be billed as additional instrument time. Additional levels of data analysis are described below.

• Protein quantification via label free or TMT assay $350/sample
• PTM for phosphorylation $400/sample 
• PTM for ubiquitin and acetylation $650/sample
• Other PTM—please inquire
• Targeted quantitative proteomics—please inquire
• Gel band identification $250/sample 

Included in standard sample analysis:

1. Peptide and Protein identification and quantification:
   Peptides are identified and quantified in either MSFragger/IonQuant, MaxQuant, or Proteome Discoverer. Peptides and proteins are reported with an identification confidence score. Proteins are reported as the total intensity of all non-redundant peptides mapped to each protein. Both peptide and protein levels are provided in the final data set.
2. Peptide and/or Protein level normalization and case-control statistics:
   Peptides are identified and quantified in either MSFragger/IonQuant, MaxQuant, or Proteome Discoverer. Match between runs is utilized to reduce missingness, and data are normalized, and assessed for technical biases. Representative high confidence and co-regulated peptides are identified and used to estimate protein levels. Protein levels are compared between groups and findings adjusted for multiple hypothesis testing.

Analyses available at an additional fee (please enquire for pricing):

1. Gene ontology analysis.
   Gene ontology enrichment analysis is used to characterize significantly up- and downregulated proteins.
2. Weighted protein co-expression network analysis.
   WGCNA is used to reduce the dimensionality of large proteomics datasets and identify co-regulated groups of proteins. These protein groups or “modules” are characterized by gene ontology enrichment analysis using WebGestalt.
3. Kinase enrichment and phosphonetwork analysis. 
   Identification of kinases that are potential drivers of altered protein phosphorylation are modeled using Kinase Enrichment Analysis. Phosphorylation Networks for Mass Spectrometry (PHONEMeS) models up- and downstream signaling networks that may be dysregulated in experimental conditions.

The Mass Spectrometry Core is now a Certified Olink Service Provider.

The Olink Proximity Extension Assay (PEA) combined with the amplification properties of DNA allows for a targeted approach to analyzing proteins while also minimizing the need for large sample volumes. The Olink Target 96 or Target 48 kits only require 1 ul of serum or plasma*. For a more detailed description of the PEA technology, please see Olink’s website at https://olink.com/our-platform/our-pea-technology/.

For a list of panels currently available for Target 48/96 please see https://olink.com/products-services/target/.

To see if your target of interest is available through the Olink Target technology, you can enter it in their search tool at https://olink.com/biomarker-search.

In order to ensure the integrity of the cold storage consumables, the investigator will purchase the Olink panel for your study, which includes all of the reagents and the microfluidic chip necessary for the panel and have it shipped directly to our site. The MSC will bill for scientist time which includes sample preparation and data analysis. Both sample preparation and data analysis time will depend on the complexity of the study, sample type and sample number.

* The Olink technology is available for many other sample types in addition to serum or plasma. Please inquire with the MSC regarding your particular sample type for more information and pricing.