Services

Protein Identification and Quantitative Proteomics

We provide global protein and post-translational modification (PTM) identification and quantitative proteomics using multiple complementary strategies, including:

  • Label-Free Quantification (LFQ)
  • Stable Isotope Labeling by Amino acids in Cell culture (SILAC)
  • Tandem Mass Tag (TMT) multiplexed quantitation
  • Dimethyl labeling (reductive dimethylation)

These approaches support differential protein and peptide abundance analyses suitable for:

  • Immunoprecipitation and affinity-purification interaction studies
  • Proximity labeling experiments (e.g., BioID, APEX)
  • Comparative proteome profiling across conditions, treatments, or genotypes

 

Targeted Quantitative Mass Spectrometry

We develop and execute targeted MRM and PRM assays for applications requiring sensitive, reproducible quantification of predefined targets, including:

  • Verification of discovery-based proteomics results
  • Quantification of selected protein or peptide panels
  • Longitudinal studies and high-throughput quantitative experiments

 

Post-Translational Modification (PTM) Discovery and Analysis

We support specialized workflows for detecting, localizing, and quantifying post-translational modifications. Early consultation is encouraged to ensure appropriate sample preparation and method selection.

Supported PTMs include (but are not limited to):

  • Phosphorylation, with optional phosphopeptide enrichment and ETD-enabled analysis for improved site localization
  • Acetylation
  • Ubiquitination
  • Glycosylation, including glycopeptide and glycan analysis using specialized methods and ETD fragmentation to preserve labile modifications

 

Sample Preparation and Cleanup

We offer a range of sample preparation and cleanup workflows designed to maximize peptide quality and minimize contamination. Services include:

  • Protein quantitation
  • SDS-PAGE
  • In-gel and in-solution digestion
  • S-Trap–based cleanup for detergent-rich or challenging samples
  • Enrichment workflows
  • TMT labeling and related chemical labeling strategies

We are happy to review buffer composition and sample compatibility prior to submission.

 

Intact Protein and Molecular Weight Analysis

We perform whole-protein molecular weight determination using complementary mass spectrometry approaches:

  • Electrospray ionization mass spectrometry (ESI-MS) for high-accuracy intact mass measurements
  • MALDI-TOF MS for rapid intact mass confirmation and screening

These analyses are suitable for confirming protein identity, detecting truncations or processing events, and assessing large post-translational modifications at the intact protein level.

 

Data Analysis and Interpretation

Results are delivered in user-friendly formats, with support for understanding and applying findings. Data analysis services include:

  • Protein and peptide identification summaries
  • Differential abundance analysis
  • PTM site identification and localization

We are also available to discuss downstream biological interpretation, follow-up experiments, and development of custom visualizations or result summaries for manuscripts and presentations.

 

Consultation and Experimental Design

We strongly encourage early engagement with facility staff, as thoughtful planning can substantially improve data quality and interpretability. We provide consultation on:

  • Sample compatibility and preparation strategies
  • Replicate structure, controls, and quantitation approaches
  • Selection of the most appropriate instrument and workflow
  • Troubleshooting existing datasets or experimental methods