Pricing

We provide fee-based proteomics services to UT Southwestern and external users, including:

  • Protein Identification Services
  • Quantitative Services
  • PTM Identification Services (post-translational modifications)

We charge for all samples, whether or not a result is obtained. The only exception is where failure is due to processing or instrumentation problems in the core. Please see our charging policy for details. Prices listed are for UTSW customers only. Customers at other universities will be charged twice the listed rate and customers at companies will be charged three times the listed rate.

To submit samples please visit our sample submission page.


 

Protein Identification Services

Protein ID – Coomassie Band

$180 per band (Orbitrap Fusion Lumos), $80 per band (Orbitrap Elite).

Service Provided: Identification of proteins in bands cut from coomassie stained SDS-PAGE gel.

Limitations: Band size is limited to 1 cm. PTM identification not included (see service 4).

Protein ID – Silver-Stain Band

$200 per band (Orbitrap Fusion Lumos), $90 per band (Orbitrap Elite).

Service Provided:  Identification of proteins in bands cut from silver-stained SDS-PAGE gel.

Limitations: Band size is limited to 1 cm. LC-MS/MS sensitivity is limited – identification of low amounts of protein from silver-stain bands may result in little or no coverage of the proteins in the gel. Use Coomassie stained gels wherever possible. Review the sample guidelines carefully before submitting silver-stain samples.

Protein ID – Complex Mixture

$180 per 5-10mm gel slice.

Service Provided: Complex mixtures may be analysed by running the mixture into the top of an SDS-PAGE gel. Bands may then be cut from the gel for LC-MS/MS analysis, with a maximum of 1 cm of gel per MS/MS run (unless you have permission from core personnel to include more). Increased coverage of very complex mixtures can be achieved by cutting and running multiple slices.

Limitations: Slices >1 cm will be refused as a single sample (unless you have permission from core personnel). Our instruments can identify 4000+ proteins from a single complex sample. Higher complexity samples must be separated into multiple slices to achieve good coverage.

In-Solution Digestion

$270 per sample.

Service provided: Customers must perform in-solution digestion themselves, following our protocol. In-solution work has significant restrictions on reagents that may be used in your experiment, to avoid contamination and damage to our instruments. In particular no detergents may be used, other than RapiGest SF (Waters) which is mass-spectrometry compatible.

All in-solution samples are subject to mandatory QC checks on our LTQ platform (using 1/5th of the sample) prior to final analysis on a more sensitive instrument. You must carefully review the detailed instructions we provide before embarking on an in-solution digestion experiment.

The in-solution workflow is necessarily restrictive to avoid contamination incidents disrupting the operation of the core. In most cases it will be cheaper, quicker, and easier to follow an in-gel workflow even if it requires working at a large scale or performing further optimization of experimental procedures.

Intact Mass Analysis 

$100 per sample.

Service Provided: Molecular weight determination of a purified protein in solution.

Limitations: Sample requirements are quite strict and can be found here. Sample must contain only one or a few proteins (with very little population distribution, i.e. multiple molecular weights for the same protein due to PTMs)

High pH Fractionation

$1500 per sample.

Service Provided: Fractionation of very complex samples using high-pH fractionation column and LC/MS/MS analysis. Samples should contain ~100 ug of protein. Please contact Esmaeil Dehghan with questions regarding this service.

Targeted Proteomics: Selected Reaction Monitoring (SRM)

$1000 for method development per protein, $90 per sample.

Service Provided: Absolute quantitation of proteins in samples. Samples are spiked with heavy-isotope labelled peptide standards for the protein of interest, which are used to determine the absolute absolute amount of a protein in a sample.

Limitations:  SRM experiments require careful experimental planning and discussion with core personnel. Customers are responsbile for purchase of heavy-isotope labelled peptide standards (we can provide a quote for these).


PTM Identification Services

PTM ID – Coomassie Band Trypsin – Single PTM & Protein

$240 per gel band

Service Provided: Identification of common specified post-translational modifications (phosphorylation, acetylation, mono/di/tri-methlyation, ubiquitination) by database search. Data analysis with Proteome Discoverer will include search for modifications specified by customer. Digest with trypsin.

Limitations: Service offered for common modifications and on strong coomassie gel bands only. PTMs identified may not be confidently localized, depending on protein sequence and peptide fragmentation.

PTM ID – Coomassie Band Alternative Enzyme – Single PTM & Protein

$280 per gel band.

Service Provided: Identification of common specified post-translational modifications (phosphorylation, acetylation, mono/di/tri-methlyation, ubiquitination) by database search. Data analysis with Proteome Discoverer will include search for modifications specified by customer. Digest with Glu-C, Asp-N, Arg-C, chymotrypsin, or elastase.

Limitations: Service offered for common modifications and on strong coomassie gel bands only. PTMs identified may not be confidently localized, depending on protein sequence and peptide fragmentation.

Custom Analysis

$60 per hour data analysis.

Custom analysis includes PTM searches on previously run gel band and complex mixture samples, as well as other bioinformatic analysis. A quote will be provided based on the services requested and the estimated time required. Please contact Mohammad Goodarzi for additional details on what services are available.


 

Quantitative Services

We offer various quantiative methods listed below. All quantitative experiments must be discussed with core staff before sample preparation begins. Experimental design  must be considered to ensure useful results. Submissions made without discussion will be rejected.

 

Protein ID & Quantitation – SILAC

$220 per 5mm gel slice.

Service Provided: Quantitative analysis of SILAC labelled simple or complex mixtures using Proteome Discoverer or MaxQuant software.

Limitations: Complex quantitative analysis require careful experimental planning and statistical analysis of results. SILAC labeling is responsibility of customer. QC runs of label incorporation etc. are required.

Protein ID & Quantitation – TMT

$1500 for 6-plex, $2000 for 10-plex analysis

Service Provided: Quantitative analysis of 6 or 10 samples using TMT (tandem mass tag) technology, using Proteome Discoverer software.

Limitations: Samples should be submitted in-solution in 50 mM triethylammonium bicarbonate with 5% SDS. Samples should have similar amounts of protein for best results. Please contact Esmaeil Dehghan for TMT sample preparation questions.

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