Proteomics Services
close up of laptop screen with scientific data displayed

We are a full-service Core and provide proteomics support from scientific consultation/experimental design and sample preparation all the way to data analysis and interpretation.

We accept a wide range of sample formats, including complex biological and clinical research samples in unprocessed form (e.g., broad variety of tissues, cells, cell supernatants and conditioned media, blood serum,  urine) as well as routine samples (e.g., SDS-PAGE gel bands, eluates from affinity chromatography or IP, beads). Pathway Analysis, N-terminal (Edman) sequencing services, and Amino Acid Analysis of proteins and peptides are also available.

When you are ready to submit samples for analysis, please download and complete the form below. Please email with any questions.

Mass Spectrometry & Protein Analysis Request Form

Sample Preparation

We accept research samples and clinical samples at any stage and prepare them for qualitative and quantitative proteomics experiments. Examples are cells or cell lysates, tissues, blood vessels, blood plasma, biopsies, and more!

Protein Identification, Profiling and shotgun proteomics

  • From single gel bands to complex protein mixtures, proteins are identified based on unique internal peptides.

Post-Translational Modifications

  • Phosphorylation site mapping (including phospho-enrichment as needed)
  • Analysis of other modifications such as methyl, acetyl, ubiquitin, citrulline, lipids, glycosylation and more!

Protein Quantitation

  • Changes in protein expression in complex protein mixtures  (label free)
  • Relative and absolute quantitation (TMT, iTRAQ, selected-, multiple- and parallel reaction monitoring)
  • Metabolic labeling (SILAC)

Characterization of Intact Proteins

  • Accurate molecular weight determination
  • Protein complexes and interactions

Protein Cleavage Sites

  • N-terminal sequencing (Edman chemistry)

Quantitation of protein/peptide content

  • Amino Acid Analysis

Sample Preparation Guidelines

Questions about how to prepare your samples? Select the document below based on your desired analysis.

List of Proteomics Services

Expert scientific consultation and experimental design

Qualitative Proteomics

  • protein identification,

  • protein profiling and interactome analysis,

  • protein sequence confirmation,

  • localization of post-translational modifications (PTMs).

  • Histone profiling

  • Glycoscreen (localization of N-Glycosylation sites)

Quantitative Proteomics

  • Protein Expression Profiling using label-free quantitation, SILAC, or TMT (labeled quantitation)

  • Targeted Proteomics (parallel reaction monitoring, PRM, “absolute” quantitation),

  • Data Independent Analysis (DIA, fast and sensitive differential quantitation for sample cohorts with at least 3 replicates)
  • Quantitation of phosphorylation sites
  • Quantitative Histone Profiling

Pathway Analysis (biological pathways, gene ontology terms, miRNAs and diseases for differentially expressed proteins)

N-terminal (Edman) protein sequencing

Quantitative Amino Acid Analysis (quantitation of total protein versus non-protein components) for proteins or peptides

Data analysis, interpretation, discussion and reporting

Mass Spectrometry Instrumentation
 Orbitrap Fusion Lumos mass spectrometer

Orbitrap Fusion Lumos mass spectrometer (Thermo Scientific) coupled to a UPLC (Waters)

  • Improved accuracy for relative quantitation (TMT, SILAC)
  • Identification of more low-level proteins with better accuracy
  • Used to analyze highly complex samples
  • Sub ppm mass accuracy
 Q-Exactive mass spectrometer

Q-Exactive mass spectrometer coupled to UPLC (Waters)

  • High throughput screening (post-translational modifications)
  • Protein ID
  • Label-free quantitation by spectral counting
  • Targeted quantitative proteomics (PRM)
Orbitrap Exploris 4800

The Orbitrap Exploris 4800

  • Increased sensitivity and dynamic range
  • Used for Data independent acquisition (DIA) and targeted MS/MS (PRM, “absolute” quantitation)
 Ultraflextreme MALDI-TOF/TOF mass spectrometer

Ultraflextreme MALDI-TOF/TOF mass spectrometer (Bruker)

  • Protein intact molecular weight analysis by MALDI-TOF and more
Contact Us
Room C570C
Medical Science Research Building (MSRB) II
1150 West Medical Center Drive
Ann Arbor, MI 48109
About Us
The Proteomics & Peptide Synthesis Core is one of the Biomedical Research Core Facilities, and a part of the Medical School Office of Research, where our mission is to foster an environment of innovation and efficiency that serves the Michigan Medicine research community and supports biomedical science from insight to impact.