Meilahti Proteomics Unit

Proteomic analyses using LC-MS/MS (Liquid Chromatography-Tandem Mass Spectrometry) are a cornerstone of modern biological research, enabling the identification, quantification, and characterization of proteins in biological samples. MPU is a core facility that provides access to advanced instrumentation, expertise, and data analysis tools. 
Sample preparation
  • Tissue and cell lysis, protein extraction, digestion (e.g. trypsin).
  • Fractionation or enrichment of specific protein subsets (e.g. phosphoproteomics, N-glycoproteomics).
  • Labeling techniques (e.g., TMT, or iTRAQ for quantitative proteomics).
LC-MS/MS analysis
  • High-resolution LC-MS/MS for protein identification and quantification.
  • Data-dependent acquisition (DDA) or data-independent acquisition (DIA) workflows.
  • Label-free or isotopically labeled peptides/proteins.
  • Targeted proteomics (e.g. SRM/MRM for specific protein/peptide quantification).
  • N-Glycoproteomics (DIA label-free proteomics and N-glycopeptidomics quantitation and DDA identification of the N-glycopeptides).
  • Other post-translational modification (PTM) analysis (e.g. phosphorylation, acetylation, ubiquitination).
Data analysis
  • Protein identification and quantification using available  softwares.
  • Bioinformatics support for pathway analysis, GO enrichment, and network modelling (on a collaborative basis).
  • Custom data analysis tailored to specific research needs, for instance for non-human species whose proteomes are not well annotated (on a collaborative basis).
Applications of LC-MS/MS in proteomics

MPU supports a wide range of applications, including:

  • Discovery proteomics: Large-scale identification and quantification of proteins in biological  samples, including differential expression of proteins between samples.
  • Targeted proteomics: Quantification of specific proteins or peptides of interest.
  • N-Glycoproteomics: A label-free proteomics and N-glycopeptidomics experiment are executed from the same samples. In N-glycopeptidomics N-glycopeptides are quantified and amino acid sequence, glycosylation site, glycan composition, in addition to some structural features are analyzed. N-glycosylation changes are compared to expression changes of the same protein in order to understand if the change is happening in total protein expression or in the glycosylation only.
  • Other PTM analysis: Characterization of other post-translational modifications.
  • Interaction proteomics: Analysis of protein-protein interactions (e.g. analysis of co-immunoprecipitation or proximity labeled samples).
  • Clinical proteomics: Biomarker discovery and validation for disease diagnosis and prognosis.
Equipment
  • Astral HRMS arriving in summer 2025! (Thermo Fisher Scientific) 
  • Q Exactive HF MS with Ultimate 3000 LC (Thermo Fisher Scientific) 
  • QTRAP 6500+ with Eksigent 400 LC (SCIEX)
  • Bravo robot (Agilent) for high-throughput sample preparation.
Typical workflow for proteomic analysis project
  1. Consultation: Discuss project goals and experimental design.
  2. Sample submission: Provide prepared samples or request sample preparation services.
  3. Return the signed sample submission form. Required prior to analyses. Submission form
  4. LC-MS/MS analysis: Core facility performs the analysis.
  5. Data delivery: MPU provides a report of the results including a list of the identified/quantified proteins. The customer provides an external disk (a few TB space) or a link to cloud to store the data.
  6. Follow-up: Collaboration on data interpretation and further analysis is possible, if needed.
Acknowledgement

To ensure the continuing support from Helsinki Institute of Life Science (HiLIFE) and BioCenter Finland, publications using the results generated at MPU should be acknowledged, for example:

We acknowledge the Meilahti Proteomics Unit (MPU) at the University of Helsinki for the proteomic analyses. MPU is supported by Helsinki Institute of Life Science (HiLIFE) and Biocenter Finland.
Collaboration

All projects on a collaborative basis need to be discussed prior to data analysis.
Prices

Costs vary depending on the type of the analysis, the number of samples. Current typical costs are:

  • Tissue or cell lysis sample preparation + LC-MS/MS analysis: 300 euros/sample, 3 runs/sample for quantification.
  • Tissue or cell lysis sample preparation + LC-MS/MS analysis: 200 euros/sample, 1 run/sample for identification.
  • Gel band analysis + LC-MS/MS analysis: 100 euros/sample.
  • Targeted  proteomic and glycan analysis will be evaluated based on the sample complexity and the time for the testing and method development.