MS-based Protein Analysis: Global Proteomics and Protegenomics, & Glycoproteomics and MS Proteomics 

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Introduction
Services
Equipment
Addresses

Introduction

Proteogenomics is rapidly developing field in biological mass spectrometry that combines proteomics information with sample specific genomic and transcriptomics information. Applications in proteogenomics include discovery of novel protein coding regions to improve genome annotation; detection of variant and mutated proteins based on DNA and/or RNA sequence data; discovery of cancer neoantigens and evaluation of the impact of genomic changes (e.g. copy number alterations, SNPs, mutations, hyper methylation) on the proteome. The facility also provides service in broad range of MS-based proteomics applications to encompass the needs of the Swedish life science community, including quantitative proteomics and proteome profiling, in-depth proteomics, interaction studies by immunoprecipition MS (IP-MS) and post-translational modification (PTM) analysis.

Contacts and service requests through: iLAB platform at KI

For instructions on how to register and login to iLab click here

Services

Personalized proteomics
Individual sequence based search database generation for variant analysis at the protein level coupled with in-depth quantitative proteome analysis.

Disease state/Variant proteomics
Database supplemented with all known SNPs and disease causing genetic alterations. (Can be used when sample specific sequence data is not available.)

Unbiased proteogenomics in any species with a sequenced genome
Six frame translation of genome generated database searches for protein coding genome annotation.

XenoProteomics
Database supplemented with peptides from disease causing pathogens.

Meta proteomics
Proteogenomics analysis based on metagenomics database generation

Plasma proteomics
In-depth global MS-based plasma proteomics

Start-up meeting and Experimental planning
Our long experience in applied proteomics provide us with a unique opportunity to assist users and in many instances refine the original experimental plan. For this reason we always offer a start-up meeting to go through the user request in detail.

Analysis of low cell numbers
(100-1000)

Services during holidays:

The core unit is not engaging/handling any new requests/projects during summer and Christmas holidays:

• Midsummer – second week of Aug (~7 weeks)
• Christmas Eve – first week of Jan (~3 weeks)

Equipment

Mass spectrometers

• MS Orbitrap Astral, Thermo Scientific
• MS Orbitrap Astral, Thermo Scientific
• MS Q Exactive HF, Thermo Scientific
• MS Q Exactive HF, Thermo Scientific.
• MS Orbitrap Exploris 480, Thermo Scientific.
• MS Tims-TOF Pro, Bruker
• MS TimsTOF HT incl Evoep, Bruker
• MS Tims-TOF SCP incl Evosep, Bruker
• MS Acquity Premier Offline UPLC, Waters

Peptide separation technologies

• HiRIEF (High Resolution Isoelectric Focusing)
• Thermo Vanquish Neo LC

Robots

• Ettan Digester (modified Gilson 215), GE Healthcare Life Science
• Biomek i7 (Beckman Coulter) robot for automated sample preparation

Addresses

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Introduction
Services
Equipment
Using the unit
Addresses

Introduction

The Proteomics Core Facility (PCF) at the University of Gothenburg provides access to expertise and instrumentation for advanced glycosylation, phosphorylation, protein quantification and many other proteomic analyses.

PCF has broad experience in the preparation and analysis of various biological materials such as tissues, cells, plasma, CSF, urine, subcellular fractions such as exosomes, proteins derived from affinity-based (immunoprecipitation) methods, BioID, expressed proteins etc. Using tandem-mass tags (TMT), samples can be analysed in parallel in a quantitative proteomics study. We apply extensive offline fractionation before LC-MS analysis accomplishing deep proteome coverage.

Analogous to proteomics, glycoproteomics is based on advanced mass spectrometry technologies that have evolved as the method of choice for global or directed analyses of glycoproteins, proteoglycans, glycosphingolipids etc in biological tissue. The concept is to characterize the glycans and/or their exact attachment sites on specific peptides, identified by their unique amino acid sequences. To accomplish this a series of enrichment strategies, ionization techniques as well as bioinformatic tools are available in the research support.

Clinical proteomics studies promoting personalised and precision medicine with large sample cohorts are performed using data-independent acquisition (DIA) and ion mobility MS in a high-throughput manner with very good data quality of the analysed proteome. Samples can be continuously collected, and studies can be going on over a long time.

Services

• Protein identification
• Quantitative or targeted proteomics
• Interaction proteomics after affinity-based approaches
• High-throughput data-independent proteomics of large cohorts
• Global and relative quantification and identification of glycopeptides
• Structural characterization of N- and O-linked glycopeptides
• Screening of released N-linked and O-linked oligosaccharides and liberated glycans from glycolipids for comparative glycomics.
• Characterization of N-linked and O-linked oligosaccharides and liberated glycans from glycolipids using exoglycosidases
• Identification and relative quantification of phosphopeptides
• Custom-made biological mass spectrometry

Equipment

Automated sample preparation

• Beckman Coulter Biomek i7
• Cellenion CellenONE

Mass Spectrometers

• Bruker timsTOF SCP
• Bruker timsTOF HT
• Thermo Orbitrap Astral
• Thermo Orbitrap Eclipse Tribrid
• Thermo Orbitrap Fusion Lumos Tribrid
• Thermo Orbitrap Fusion Tribrid
• Thermo QExactiveHF
• Thermo LTQ Orbitrap

Peptide Separation

• Online: Thermo Easy nLC1200 systems
• Online: Evosep One nLC systems
• Online: Thermo Vanquish Neo HPLCs
• Offline: high pH UPLC fractionation: Thermo Dionex Ultimate 3000

Using the unit

When you are planning a project for analyses at PCF, please contact us via pcf@gu.se. We are happy recommending suitable methodology and study design in order to create results of high quality and scientific impact. After filling in our sample submission form you are welcome to deliver your samples to our facility.

Addresses