Pricing

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

  • Protein Identification Services
  • Intact Protein Mass Analysis
  • 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 and UT-system customers only. Customers at other universities will be charged twice the listed rate, customers at companies will be charged three times the listed rate, and UT Southwestern BioCenter tenants are charged 2.5-times the listed rate.

To submit samples please visit our sample submission page.

Prices listed are effective August 9, 2023


Protein Identification Services

Protein ID & Quantitation – Trypsin

$204 per sample or gel band (Orbitrap Fusion Lumos), $82 per sample or gel band (QExactive HF).

Service Provided: Identification of proteins from solutions, on-beads, or from bands cut from Coomassie stained SDS-PAGE gel.

Limitations: Band size is limited to ~1 cm. PTM identification not included.

Protein ID & Quantitation – Alternative Enzyme

$245 per sample of gel band (Orbitrap Fusion Lumos), $122 per sample or gel band (QExactive HF).

Service Provided: Identification of proteins from solutions, on-beads, or from bands cut from Coomassie stained SDS-PAGE gel. Please contact core to discuss the appropriate enzyme for your sample(s).

Limitations: Band size is limited to ~1 cm. PTM identification not included.

Protein ID & Quantitation – Trypsin – Silver-Stain Band

$224 per band (Orbitrap Fusion Lumos), $92 per band (QExactive HF).

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 & Quantitation – Alternative Enzyme – Silver-Stain Band – Lumos

$265 per band (Orbitrap Fusion Lumos)

Service Provided: Identification of proteins in bands cut from silver-stained SDS-PAGE gel. Please contact core to discuss the appropriate enzyme for your sample(s).

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

Protein ID and Quantitation – Trypsin – Complex Mixture

$204 per sample, 90 minute gradient. $306 for 3 hour gradient.

Service Provided: Complex mixtures may be analyzed by submitting a solution, beads, or by running the mixture into the top of an SDS-PAGE gel (our preferred method).  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, or by performing high-pH peptide fractionation.

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.

Intact Mass Analysis 

$31 per sample for peptides in mass spec compatible buffer.

$102 per sample for proteins or peptides, requiring desalting.

Service Provided: Molecular weight determination of a purified peptide or 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

$1020 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.

HPLC In-Depth Fractionation (for >8 fractions)

$1020 for first 8 fractions, $102/additional fraction

Service Provided: Fractionation of very complex samples using HPLC and LC/MS/MS analysis. Samples should contain ~100 ug of protein.

Targeted Proteomics: Selected Reaction Monitoring (SRM)

$1020 for method development per method, $92 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 responsible for purchase of heavy-isotope labelled peptide standards (we can provide a quote for these).


PTM Identification Services

PTM ID – Trypsin – Lumos

$265 per sample

Service Provided: Identification of common specified post-translational modifications (phosphorylation, acetylation, mono/di/tri-methylation, ubiquitination) by database search. Data analysis with Proteome Discoverer will include search for modifications specified by customer. Protein digestion will be performed 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 – Alternative Enzyme – Lumos

$306 per sample.

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.

PTM ID – Coomassie Band Trypsin – Glycosylation

$357 per gel band

Service Provided: Identification of protein glycosylation and glycan composition on peptides by database search. Data analysis with Proteome Discoverer and Byonic. Digest ion is performed with trypsin.

Limitations: Service offered for strong Coomassie gel bands only or solutions with sufficient glycoprotein concentration. PTMs identified may not be confidently localized, depending on protein sequence and peptide fragmentation.

Phosphopeptide Enrichment

$153 per sample.

Service Provided: Enrichment of phosphorylated peptides from complex samples using TiO2 and Fe-NTA columns. Samples should contain at least 1 mg of protein. Please contact Xuemei Luo with questions regarding this service.

Ubiquitination Enrichment

$300 per sample.

Service Provided: Enrichment of ubiquitinated peptides from complex samples using the PTMScan® Ubiquitin Remnant Motif (K-ε-GG) Kit. Samples should contain at least 1 mg of protein. Please contact Xuemei Luo with questions regarding this service.

Custom Analysis

$61 per hour data analysis.

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


Quantitative Services

We offer various quantitative 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

$224 per sample.

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

$1530 for 6-plex, $2040 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 appropriate lysis buffer, such as 50 mM triethylammonium bicarbonate with 5% SDS, or RIPA buffer. Other buffers may also be accepted. Samples should have similar amounts of protein for best results. Please contact Xuemei Luo for TMT sample preparation questions.

Protein ID & Quantitation – TMTpro

$3264 for 16-plex analysis, $3672 for 18-plex analysis

Service Provided: Quantitative analysis of up to 18 samples using TMTpro (tandem mass tag) technology, using Proteome Discoverer software.

Samples should be submitted in-solution in appropriate lysis buffer, such as 50 mM triethylammonium bicarbonate with 5% SDS, or RIPA buffer. Other buffers may also be accepted. Samples should have similar amounts of protein for best results. Please contact Xuemei Luo for TMTpro sample preparation questions.

Other Services

Deparaffinization of FFPE Blocks

$510 for supplies for up to 20 samples, $51/sample for removal of paraffin from FFPE samples

Service Provided: Removal of paraffin from FFPE block slices. This cost is in addition to the standard sample prep costs.

Human/Mouse Plasma/Serum Abundant Protein Depletion

$120 per sample

Service Provided: Depletion of the most abundant proteins in human plasma or serum using the Thermo Top14 plasma depletion kit, or of albumin and IgG in mouse plasma plasma or serum using the Proteome Purify 2 Mouse Serum Immunodepletion Resin.

Limitations: Plasma or serum must be from human or mouse origin. Not compatible with other organisms.

LC/MS only

$102 per sample for Lumos, $51 per sample for QExactive HF

Service Provided: LC-MS/MS run, 90 minutes, of an already digested sample. No data analysis is included. Core will send the raw data files to the customer.

Limitations: No data analysis or sample prep included.

MS Proteomics Services