Mass Spectrometry

The Mass Spectrometry Core at USC School of Pharmacy serves the scientific research community at USC as well as external collaborators. Our Core is equipped with state-of-the-art instruments for imaging mass spectrometry (IMS), high-throughput screening, and quantitative metabolomic and proteomics. Our Core is dedicated to actively collaborate with internal and external research groups in providing comprehensive service in MALDI imaging and high-throughput screening of small molecules, peptides, and proteins using mass spectrometry.

Instrumentation: Bruker Rapiflex Tissuetyper, HTX M5 sprayer, Thermo Fisher Q-Exactive Orbitrap equipped with both ESI and APCI ion sources equipped with a nano-LC system, Sciex Q-Trap 6500.

Services: Our consultations and services are detailed as follows:

    1. Mass spectrometry imaging:
      1. Regular tissue freezing with liquid nitrogen conserving tissue shape and integrity
      2. Cryosectioning of frozen and FFPE tissues
      3. Sample preparation for MALDI imaging including regular washing, desalting, and lipid/protein/dye removal.
      4. MALDI matrix purification and solution preparation
      5. Robotic matrix deposition on tissue sections using HTX M5 sprayer
      6. MALDI imaging of various tissue types at high spatial resolution (20 um) and super high speed (40 pixels per second).
      7. On-tissue trypsin digestion for protein identification and proteomics studies
      8. MALDI MS/MS for compound/protein identification
      9. Targeted small molecule/drug imaging and identification
      10. Comprehensive data analysis such as heat map visualization, pathology-guided IMS, and statistical analysis
    2. Mass spectrometry-based high-throughput screening:
      1. Preparation of enzymatic reaction such as enzyme/substrate stock handling and preparation, enzyme/small molecule dispensing and incubation, reaction quenching and aliquoting.
      2. Generating dose-response source plates with serial dilutions up to 16 different concentrations
      3. Rigorous data analysis including IC50 calculations, single point and DR curve plotting
      4. Z’ calculations for plate-to-plate variations
      5. Hit identification
    3. Proteomics and quantitative mass spectrometry:
      1. 1D SDS PAGE
      2. Tryptic and peptic digestion of proteins, both in solution on-gel digestion
      3. LC/MS of intact proteins
      4. LC/MS/MS for protein identification and post-translational modification (PTM) analysis
      5. Site-specific modifications of proteins such as lysine acetylation and methylation.
      6. MRM and PRM assays for metabolite, drug, and protein quantitation in biological samples such as plasma and cell culture.


Bruker Rapiflex/HTX sprayer

Type of service Fee (SoP) Fee (USC) Fee (External)
Sample storage/handling $5/sample $7/sample $12/sample
Cryo-sectioning $8/tissue $10/tissue $16/tissue
MALDI spotting* $30/sample $35/sample $40/sample
MALDI imaging (IMS)** $350/sample $370/sample $400/sample
IMS data analysis $50/sample $55/sample $65/sample
Spraying custom solutions $10/sample $15/sample $25/sample
High-throughput screening (HTS) $10/hour $15/hour $25/hour
HTS data analysis $5/hour $7/hour $12/hour
Assay development҂ $50/hour $55/hour $60/hour

*An additional $50/sample will be charged if extraction and processing is performed.
**An additional $50/sample will be added for on-tissue tryptic digestion.
May vary based on complexity of analysis
Subject to approval by Dr. Abdolvahabi
҂Subject to change depending on the complexity of samples.

 Thermofisher Q-Exactive Orbitrap/nLC1000

Type of service Fee (SoP) Fee (USC) Fee (External)
Sample storage/handling $5/sample $7/sample $12/sample
Instrument time

(trained users)

$10/hour $15/hour $20/hour
Untargeted LC/MS҂ $40/sample $45/sample $50/sample
LC/MS/MS҂ $50/sample $55/sample $60/sample
Data analysis $20/hour $25/hour $30/hour
Intact protein MW determination** $30/sample $35/sample $45/sample
In-gel trypsin digestion (coomassie blue stain)** $100/sample $120/sample $150/sample
In-solution trypsin digestion** $120/sample $125/sample $135/sample
Assay development҂ $50/hour $55/hour $60/hour
Post-translational modification Contact Dr. Abdolvahabi Contact Dr. Abdolvahabi Contact Dr. Abdolvahabi

* Contact Dr. Abdolvahabi for training.
**Includes data analysis.
҂Subject to change depending on the complexity of samples.

Sciex Q-trap 6500

Type of service Fee (SoP) Fee (USC) Fee (External)
Sample storage/handling $5/sample $7/sample $12/sample
Instrument time

(trained users)*

$10/hour $15/hour $20/hour
Untargeted LC/MS҂ $40/sample $45/sample $50/sample
LC/MS/MS҂ $50/sample $55/sample $60/sample
Quantitative MRM assay†҂ $60/sample $65/sample $75/sample
Data analysis $20/hour $25/hour $30/hour
Solid-phase extraction for MRM assay $30/sample $35/sample $45/sample
Derivatization for MRM assay҂ $10/sample $15/sample $25/sample
Assay development҂ $50/hour $55/hour $60/hour

*Contact Dr. Abdolvahabi for training.
**Includes data analysis
Includes simple liquid-liquid extraction.
҂Subject to change depending on the complexity of samples.

For all requests

A quote will be generated with estimated cost breakdown and time of completion upon receipt of completed service request form.

Sample priority policy

Type of project Affiliation Number of samples Priority
Funded SoP >100 4 – Highest
Apply for funding USC 50-100 3
Unfunded Non-USC (external) <50 2
Pilot/method development 1 – Lowest


In case different projects are submitted to the Core at similar times and require fast turnarounds, the sum of priority scores determines which project would get priority in implementation.