Proteomics Services

Proteins are identified after in-gel or in-solution digestion. Proteins can be optionally fractionated prior to digestion. The cost for this analysis depends on the complexity of sample preparation and the number of samples that are being analyzed.

Pricing

WashU: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External Academic/Nonprofit: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External For-Profit Industry: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

Instruments Used

Orbitrap Eclipse Tribrid

Orbitrap Exploris 480

timsTOF Pro 2

Orbitrap Astral

Co-immunoprecipitation (CO-IP) is a popular technique to identify physiologically relevant protein-protein interactions by using target protein-specific antibodies to indirectly capture proteins that are bound to a specific target protein. These protein complexes can then be analyzed to identify new binding partners, binding affinities, the kinetics of binding and the function of the target protein.

Pricing

WashU: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External Academic/Nonprofit: Starting at $ (depending on the umber of samples submitted and length of LCMS gradient)

External For-Profit Industry: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

Instruments Used

Orbitrap Eclipse Tribrid

Orbitrap Exploris 480

timsTOF Pro 2

Proximity labeling relies on a labeling enzyme that can biotinylate nearby biomolecules promiscuously. Using the high affinity of “biotin-streptavidin”, this technique has been used for identifying the components of novel cellular structures and for determining protein-protein interaction partners. Depending on the species of labeling enzyme, biotin labeling can be achieved through several different methods.

BioID: BioID is a mutant E. coli biotin ligase that catalyzes the activation of biotin by ATP. The activated biotin is short-lived and thus can only diffuse to a region proximal to BioID. Labeling is achieved when the activated biotin reacts with nearby amines, such as the lysine sidechain amines found in proteins.

TurboID: TurboID is a biotin ligase engineered via yeast surface display directed evolution. TurboID enables ~10 minute labeling times instead of the ~18 hour labeling times required by BioID.

APEX: APEX is an ascorbate peroxidase derivative reliant on hydrogen peroxide for catalyzing the oxidation of biotin-tyramide, also known as biotin-phenol, to a short-lived and reactive biotin-phenol free radical.

APEX2: APEX2 is a derivative of APEX engineered via yeast surface display directed evolution. APEX2 shows improved labeling efficiency and cellular expression levels.

RIME: RIME can be used in parallel with ChIP-seq experiments to provide information on both the cistrome and interactome for a given protein. It uses formaldehyde fixation to stabilize the protein complex, and cross-linked protein complexes are affinity purified by bead-bound antibodies and analyzed by MS.

ChIP-MS: ChIP-mass spectrometry captures chromatin bound protein interactions and modified histones associated with a protein of interest (a bait protein). We provide consultation for study design and MS analysis.

Pricing

WashU: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External Academic/Nonprofit: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External For-Profit Industry: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

Instruments Used

Orbitrap Eclipse Tribrid

Orbitrap Exploris 480

timsTOF Pro 2

Protein quantification requires a consultation to help design the experiment first. Depending on the project and budget, we can use a variety of methods to achieve the protein quantification analysis.

1. Heavy Isotope label-based Quantification

1) Metabolic Label: SILAC (Stable Isotope Labeling of Amino Acids in Cell Culture)

Best suited for cell culture system, up to 3 states to compare.

2) Isobaric Label: TMT/iTRAQ

Comparison for >10 states, fewer MS runs, please add reagents cost

2. Label-free Quantification (LFQ)

Technical replicates required, no reagent needed.

Pricing

WashU: Contact us for a quote

External Academic/Nonprofit: Contact us for a quote

External For-Profit Industry: Contact us for a quote

Instruments Used

Orbitrap Eclipse Tribrid

Orbitrap Exploris 480

timsTOF Pro 2

When you want quantify specific target peptides or proteins, 'Targeted Proteomics' can be used. It requires a method development for the most accurate quantification of targets. After the protocol is established, it offers a high throughput at low cost to quantify up to hundreds of proteins.

There is a method development cost and heavy peptide cost to consider in order to establish the assay. The cost would vary depending on the number of analytes and whether or not you want absolute quantitation (i.e. There are exactly 10.25 picomoles of your peptide in this sample) or relative quantitation (i.e. The level of your peptide in sample A is four-fold higher than in sample B). Depending on the experiment design, we can either use MRM or PRM.

Typically, discovery experiments using untargeted methods lead to targeted methods for a validation stage which require less sample and less time on high throughput scale 

Pricing

WashU: Contact us for a quote

External Academic/Nonprofit: Contact us for a quote

External For-Profit Industry: Contact us for a quote

Instruments Used

TSQ Altis Plus

Orbitrap Exploris 480

The Epiproteomic Histone PTM Panel provides rapid profiling of site-specific methylation and acetylation states on histones. At present, more than 9o modification states on Lysine residues can be tracked and quantified by triple-quadrupole based MRM assay.

Sample requirements for histone assay:

1) Cells Requirement: 1 – 5million

2) Tissue Requirement: 25 – 100mg

Pricing

WashU: $

External Academic/Nonprofit: $

External For-Profit Industry: $

Instruments Used

TSQ Altis Plus

Phosphorylation is a key reversible modification that regulates protein function, subcellular localization, complex formation, degradation of proteins, and therefore cell signaling networks. In this assay, Phosphopeptides are enriched using titanium dioxide (TiO2 ) and high pH reverse phase fractionation into four fractions prior to being analyzed by orbitrap-based MS. The phosphopeptides are identified and site-specific quantification of phosphorylation is achieved by MaxQuant software.

Sample requirements for phosphoproteomics:

Start soluble protein amount, 5-6mg

Pricing

WashU: $

External Academic/Nonprofit: $

External For-Profit Industry: $

Instruments Used

Orbitrap Eclipse Tribrid

Orbitrap Exploris 480

timsTOF Pro 2

PTMScan® Technology employs a proprietary methodology from Cell Signaling Technology (CST) for peptide enrichment by immunoprecipitation using a specific bead-conjugated antibody in conjunction with LC-MS for quantitative profiling of post-translational modification (PTM) sites in cellular proteins. These include ubiquitination (UbiScan®), acetylation (AcetylScan®), methylation (MethylScan®), and phosphorylation (PhosphoScan®) among others.

Sample requirements for PTMScan:

Grow approximately 1-2 x 108 cells for each experimental condition (enough cells to produce approximately 10-20 mg of soluble protein).

Pricing

WashU: $ (Plus PTMSCan Kit)

External Academic/Nonprofit: $ (Plus PTMSCan Kit)

External For-Profit Industry: $ (Plus PTMSCan Kit)

Instruments Used

Orbitrap Eclipse Tribrid

Orbitrap Exploris 480

timsTOF Pro 2

IgG heavy chain carries an N-glycan attached to each Asn297 residue of the IgG1-Fc modulating its biological function. The heterogeneity of glycan moieties has implicated on the stability, conformation, aggregation, and effector function of (therapeutic) antibodies. At present, we can detect and quantify 17 different glycoforms (attached to the IgG1-Fc) simultaneously in one MS acquisition.

Pricing

WashU: $

External Academic/Nonprofit: $

External For-Profit Industry: $

Instruments Used

Orbitrap Eclipse Tribrid

Orbitrap Exploris 480

timsTOF Pro 2

Cross-linking mass spectrometry (XL-MS) is a powerful technique used to study protein-protein interactions and protein structures in solution. It involves chemically cross-linking proteins at or near interacting sites, typically using a bifunctional cross-linker, which forms covalent bonds between amino acid residues that are in close proximity.

After cross-linking, the proteins are enzymatically digested into peptides, preserving the cross-linked residues. These cross-linked peptides are then analyzed using mass spectrometry to identify the amino acid residues involved in the interaction.

Pricing

WashU: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External Academic/Nonprofit: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External For-Profit Industry: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

Instruments Used

Orbitrap Eclipse Tribrid

MTAC has established a Native Mass Spectrometry workflow specifically tailored for determining the ratio of antibodies to drugs in Antibody-Drug Conjugates (ADCs). This precise determination is instrumental in designing ADCs that enhance the therapeutic index by delivering chemotherapeutics preferentially to target cells while minimizing impact on normal cells.

Pricing

WashU: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External Academic/Nonprofit: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External For-Profit Industry: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

Instruments Used

Orbitrap Exploris 480 Biopharma with FAIMS

We can provide relative quantitation of antibodies, detect a number of modifications, and tandem MS information to confirm its sequence.

Typical amounts of material required are 50 uG solution of each antibody dialyzed against 100 mM ammonium acetate overnight at 4°C.

Pricing

WashU: Contact us for a quote

External Academic/Nonprofit: Contact us for a quote

External For-Profit Industry: Contact us for a quote

Instruments Used

Orbitrap Eclipse Tribrid with FAIMS

Orbitrap Exploris 480 Biopharma with FAIMS

Top-down proteomics include the ability to detect degradation products, protein isoforms, sequence variants, combinations of post-translational modifications. (Native) TD is tailored to the analysis of semi-pure proteins with minimal non-target protein contamination. Examples of good candidates for this approach include recombinant-expressed proteins, in vitro enzyme assay experiments, and the characterization of bioactive peptides.

Pricing

WashU: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External Academic/Nonprofit: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

External For-Profit Industry: Starting at $ (depending on the number of samples submitted and length of LCMS gradient)

Instruments Used

Orbitrap Eclipse Tribrid with FAIMS

Orbitrap Exploris 480 Biopharma with FAIMS

Work performed by the MTAC should be acknowledged as shown below:

"Mass Spectrometry analyses were performed by the Mass Spectrometry Technology Access Center at the McDonnell Genome Institute (MTAC@MGI) at Washington University School of Medicine, supported by the Diabetes Research Center/NIH grant P30 DK020579, Institute of Clinical and Translational Sciences/NCATS CTSA award UL1 TR002345, and Siteman Cancer Center/NCI CCSG grant P30 CA091842."

Contact MassSpec@wustl.edu to get more information