Services

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. External customers should contact the core for pricing.

To submit samples please follow our Sample & Submission Guidelines.


 

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 5mm. 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 5mm. 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 5mm of gel per MS/MS run. Increased coverage of very complex mixtures can be achieved by cutting and running multiple slices.

Limitations: Slices >5mm will be refused as a single sample. Our instruments can identify 1000+ 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 of a few proteins (with very little population distribution, i.e. multiple moleuclar weights for the same protein due to PTMs)


PTM Identification Services

PTM ID – Coomassie Band Trypsin – Single PTM & Protein

$240 per gel band

Service Provided: Identification of a single common specified post-translational modifications (phosphorylation, acetylation, mono/di/tri-methlyation) on a single protein by database search. Data analysis with CPFP will include search for modifications specified by customer, and PTM localization scoring. 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 a single common specified post-translational modifications (phosphorylation, acetylation, mono/di/tri-methlyation) on a single protein by database search. Data analysis with CPFP will include search for modifications specified by customer, and PTM localization scoring. 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.

PTM ID – Custom Analysis

Base price ($240/$280) as above + $60 per hour data analysis.

Custom analysis is required for identification of multiple PTMs, and/or PTMs on multiple proteins in simple or complex mixtures. Also unrestricted PTM search. Base price includes 30 minutes of data analysis.

Free PTM ID Training

Don’t want to pay for custom PTM analysis? We will offer free training so you can analyze your data yourself using our analysis pipeline.


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 – SINQ Spectral Index

FREE with Complex Mixture Identification service.

Service Provided:  Spectral index quantitation of proteins in complex mixture samples and comparison between samples. Results available online in CPFP analysis pipeline.

Limitations: Accuracy of quantitation is lower than labelled methods or precursor label-free methods. Accuracy will depend on complexity of sample and abundance of protein. Generally suitable for identifying large change between samples, genuine interactors in Co-IP vs control etc.

Protein ID & Quantitation – SILAC

$220 per 5mm gel slice.

Service Provided: Quantitative analysis of SILAC labelled simple or complex mixtures using CPFP analysis pipeline 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.

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