Proteomics

Related services

• Genome-wide bioinformatics and computational systems biology
• Transcriptomics, toxicogenomics and other genomics
• Biomarker discovery and validation
• In vivo disease models
• Molecular biology
• Virtual HTS, ligand, target, and reverse docking

Peptide mass fingerprinting for protein identification with MALDI TOF-TOF mass spectroscopy

Peptide Mass Fingerprinting (PMF) is a fastest and cheap method of protein identification. The procedure involves optional protein enrichment by e.g. PAGE followed by excision of the band from the gel, alternatively protein identification can also be done directly from any protein sample in dissolved form.
Samples are digested with trypsin and the peptides are analyzed by a MALDI-TOF (Bruker Ultraflex II). MS analysis of the tryptic peptides will be conducted and the PMF data will be searched against protein database.
Please follow this link to retrieve a detailed fact sheet of the Peptide mass fingerprinting for protein identification with MALDI TOF-TOF mass spectroscopy service

Peptide mass fingerprinting for protein identification with tandem mass spectroscopy (MS/MS)

This mass spectrometry technique is an extension of peptide mass fingerprinting technique which is used mainly for confirmation of identity or to identity post- translational modification like phosphorylation, glycosylation etc.
We utilize a MALDI-TOF/TOF technique (Bruker Ultraflex II), which is a quick, sensitive and reliable method for protein identification, allowing identification of unknown protein at low fmol levels. The second mass detector is analyzing the fragmentation of a particular precursor ion at different amide bonds and generating spectra of daughter ions. This allows the generation of the actual sequence data of the unknown peptide for its identification.
Please follow this link to retrieve a detailed fact sheet of the Peptide mass fingerprinting for protein identification with MS/MS service

Protein characterization - intact molecular weight analysis

The accurate mass analysis of proteins is typically needed when studying the post-translational modifications (PTM). Examples include analysis of the mass heterogeneity of glycoproteins, different phosphorylated variants, presence of ubiquitinylation and sumoylation, attachments of lipids or presence of disulphide (Cys-Cys) bridges. Accurate mass analysis can also be used to study the presence of alternatively spliced forms of the proteins as well as e.g. to check the batch to batch consistency/variability of therapeutic proteins or monoclonal antibodies.
The mass profile of a chosen protein is measured by ESI-MS mass spectrometry technique using Electrospray Ultra- High Resolution tandem TOF (UHR-Qq-TOF) (Bruker MaXis). The mass spectra will be deconvoluted and further used to report the accurate observed mass values.
Please follow this link to retrieve a detailed fact sheet of the Protein characterization - intact molecular weight analysis service

Protein modification monitoring or monitoring of selected proteins by MRM mass spectroscopy

Multiple Reaction Monitoring (MRM) assay is considered the most selective and sensitive mass spectrometry technique to detect proteins of interest with enhanced specificity using selective ion monitoring scanning mode. During this process, complex biological protein samples will be enzymatically digested and peptides of specific masses are selected and all others are excluded.
The application of LC/MRM (SRM)-MS is a versatile tool for the discovery phase, quantitation of proteins during validation phase or post-translational modification profiling in complex biological samples. The main advantage of this technology involves in mass screening of biological samples for biomarker validation or quantitation. It rules out the need for specific antibodies or running any gels for protein separation or western blotting. Transitions e.g. for potential serine/threonine or tyrosine phosphorylations will be predicted for a given protein in a given biological sample and quantified by MRM triggered scanning will be conducted on LC-MS/MS for further validation.
Please follow this link to retrieve a detailed fact sheet of the Protein MRM analysis service

Protein characterization - Characterization of Post-translational Modifications (PTM)

Post-translational modification (PTM) is a chemical modification of a protein after its translation often extending the range of functions of the protein by attaching to it other biochemical functional groups such as acetate, phosphate, various lipids and carbohydrates, changing the chemical nature of an amino acid or by structural changes via the formation of disulfide (Cys-Cys) bridges.
Among different types of PTMs, phosphorylations and glycosylations are the most common modifications. Other common PTMs include ubiquitinylation and sumoylation.
PTMs are analyzed in various applications, like studying signal transduction cascades, protein degradation tagging and analysis of the occupancy of the glycosylation sites.
This technique involves MS/MS fragmentation to determine the site and/or percentage of post-translational modification. PTM site are mapped with MS/MS fragmentation using a MALDI TOF/TOF mass spectrometer (Bruker Ultraflex II) or Electrospray Ultra-High Resolution tandem TOF (UHR-Qq-TOF) (Bruker MaXis).
Please follow this link to retrieve a detailed fact sheet of the Characterization of PTMs analysis service

Protein quantitation by iTRAQ- isobaric Tag for Relative and Absolute Quantitation

Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) is a non-gel based multiplexed protein quantitation technique that provides relative and absolute measurements of in theory all peptides from different samples/treatments.
Trypsin digested iTRAQ labelled samples are pooled, fractionated and analyzed by liquid chromatography and analysed by tandem mass spectrometry (LC/MS/MS). A database search is then performed using fragmentation data to identify the labelled peptides and hence the corresponding proteins whilst the iTRAQ mass reporter ion is used to relatively quantify the peptides. Quantitation of protein from multiple samples can be achieved in the same run.
Please follow this link to retrieve a detailed fact sheet of the iTRAQ qantitation service

Proteome mapping (Global protein profiling) with Gel-LC-MS/MS

The main objective of proteome mapping is to profile the protein content of a given biological sample. Application of this technique will be mainly used to identify differentially expressed proteins different samples.
Gel-nano-LC-MS/MS (GeLC/MS) is a powerful and simple approach for proteomic analyses. Samples are run on 1-D SDS-PAGE to resolving proteins into protein bands of different molecular weights. After separation, protein bands are excised from the gel lane into equally sized segments. The greater the number of protein bands, the deeper the coverage of the sample. Each protein band is then in-gel digested with trypsin, and peptides either analyzed by a MALDI TOF/TOF mass spectrometer (Bruker Ultraflex II) or separated by automated online strong cation exchange (SCX) and reversed phase (C18) liquid chromatography (2D-LC) and identified using with electrospray ultra-high resolution tandem TOF (UHR-Qq-TOF) (Bruker MaXis), known as MudPIT 2D-LC-MS/MS method.
Please follow this link to retrieve a detailed fact sheet of the Gel-LC-MS-MS profiling service

Proteome mapping (Global protein profiling) with LC-MS/MS (label-free mass spectrometry)

Label-free mass spectrometry is a totally non-gel based technique that can be also use for global protein profiling using full scan mode of LC-MS/MS. This technique also provides relative quantitation in expression of protein. This technique has advantages in terms of simplified sample handling and processing, low sample amount requirement (in μl) and no need of metabolic or chemical labeling.
Trypsin digested peptides are separated by automated online strong cation exchange (SCX) followed by reversed phase (C18) liquid chromatography (2D-LC) and identified using electro-spray ultra-high resolution tandem TOF (UHR-Qq-TOF) (Bruker MaXis), known as MudPIT 2D-LC-MS/MS method.
Please follow this link to retrieve a detailed fact sheet of the LC-MS/MS profiling service

Protein Biomarker Discovery and Validation Platform

We also offer a comprehensive protein biomarker discovery and validation platform for our customers. This platform combines the study design, proteomics biomarker discovery, methods development and validation phases. Please follow this link to read more on biomarker discovery and validation platform.

Our proteomics services are coupled with our bioinformatics and computational systems biology expertise. This allows us to offer our expertise already from the experiment planning phases: how many arrays should be used, what types and number of replicates should be done, how the sampling, sample processing and quality control should be done etc.
Correct planning of the genome wide experiments is very important in order to achieve the aimed statistical confidence and end-results of the experiments. We offer the experimental planning consultation free of cost when coupled with the genome-wide profiling service.

Proteomics for biologics discovery

We offer our proteomics expertise also for companies discovering protein based biological drugs. We provide customized services in e.g. protein stability and kinetics in different biological fluids and tissue extracts, protein translocation like placental perfusion transport.

All our services are tailored to the customers need. Click here for our other discovery biology and discovery informatics services.