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The Proteomics and Metabolomics Program

Research Pipelines

Let Us Help you Doing a Great Research

The proteomics unit in CCHE-57357 is the first proteomics unit in Egypt and Middle East. It provides a variety of professional services and collaboration to researchers in the field of protein identification and quantification, including several major package such as:

Our “365” proteome profiling service allows identification and quantification of 3000- 6,000 proteins from as little as 50- 100 K cells or 10-20 micrograms of tissue extract (depending on several parameters). This label-free profiling protocol is based on a reverse phase chromatographic fractionation coupled with an up to date TripleTOF Mass spectrometry . Total protein is extracted from the sample and digested, then purified peptide is fractionated with nanoLC chromatography coupled with TripleTOF, a sensitive core instrument configuration. With such workflow, we can obtain an average of ~30k peptide spectra in 30 min-3 hours of sequencing time. These spectrometry data routinely identifies 1,000-6,000 proteins in each experiment. The sensitivity of the profiling methodology is suitable for the cost effective analysis of small scale or clinical samples. The label-free mass spectrometry-based protein quantification is standard with this service and can be effectively used for differential protein expression analysis.

A routine sequencing of protein samples for protein identification and verification purpose could be achieved using this method. In simple, one dimensional electrophoresis using SDS-PAGE electrophoresis is used to fractionate proteins based on their molecular weight, this step is followed by In-Gel trypsin digestion of designated band or the whole lane. Extracted peptides are subjected to mass spectrometric analysis using our powerful and sensitive TripleTOF.

We provide PTM (post- translational modification) analysis of a crude protein sample or affinity purified endogenous or ectopically expressing a single recombinant protein. The service includes targeted PTM or shotgun screening on the possible modification existing in the sample with their exact sequence and location.

Here, we capture the targeted protein using immuno-precipitation, then sample is analyzed in depth using LC-MS/MS. Targeted protein are sequenced and label free quantified as a routine work.

We perform SILAC and dimethyl labeling relative quantification of experimental samples. For example, protein extract from 3 different groups are labeled differently as light, intermediate and heavy. Sample are pooled together and analyzed with nanoLC-MS/MS technology to understand the dysregulation of a certain protein(s) between different experimental groups.

If the researcher wants to investigate a certain protein(s) in his sample, single reaction monitoring or multiple reaction monitoring is the perfect choice. Here we feed the mass spectrometry with the protein information where it keeps tracking this protein in the sample until it detects it and allows it for fragmentation, identification, and then relative/absolute quantitation it in the sample.

SWATH (https://sciex.com/technology/swath-acquisition), is a next generation proteomics analysis relay on independent data acquisition. SWATH is considered as one of the premier mass spec acquisition strategies for identification and quantitation of analytes complex samples. SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). In CCHE, we professionally identify proteins using SWATH to enable comprehensive, sensitive and accurate result.

We have a complete pipeline for pharmaceutical analysis. The sensitivity of LC-MS technology can precisely determine the identities and quantities of compounds within your sample. Mass spectrometry coupled with liquid chromatography (LC-MS) delivers analytical speed, sensitivity, and selectivity for a variety of applications in pharmaceutical testing including Therapeutic drug monitoring (TDM) and pharmacokinetics. Beside it also used in R& D wings (research and development).


LC-MS/MS analysis in clinical diagnosis and health industry:

We have a pipeline for small molecule detection based on fragmented/sequence molecule with high resolution LC-MS/MS technology. Many disorders to body metabolism alteration in body fluids are diagnosed by LC-MS/MS analysis of concerned fluids through targeted or untargeted metabolomics.


LC-MS/MS applications in scientific research:

LC-MS/MS system is a mandatory tool in most of the labs involved in research. The fields of research include medical, biological, chemical, biochemical, phytochemical (plant chemical research). It use this application to analyze and quantify the molecules. Components with similar chemistry and properties are easily distinguished by this method. Due to the principle of separation in HPLC similar molecules get separated and hence their detection, identification and quantification becomes easier using mass.


LC-MS/MS applications in Pharmaceutical and Analytical Fields:

It plays an important and critical role in the field of pharmaceutical industries and analysis, since it is used to test the products and to detect the raw ingredient used to make them i.e., qualitative and quantitative analysis. In pharmaceutical industry,LC-MS/MS analysis is prominently used in quality control.


  • In quality control, it is used to check if the prepared or manufactured products are in compliance with the specified standards as per the pharmacopoeia and other drug regulating bodies. For quality control, the manufactured product must comply with the quality guidelines referring to pharmacopoeia will give an idea of how the peak of the drug in the formulation should look, at the specified solvents and mobile phases used. If the peaks do not correspond to those shown in pharmacopeia, the batch cannot be passed for quality check.

  • In R & D as discussed in research before, it is used to identify the specific molecule or component in mixture under research. Further it is used for bioavailabilty studies, drug release from the formulation, dissolution studies etc. After a formulation is designed, the drug release over a period of time is tested in bioavailabilty studies. Then the sample released is taken and injected into HPLC system to note the individual molecules released in terms of quantity.

  • Also any new molecule under development or preclinical trial, are analyzed to see their concentration in the blood after certain intervals of administration. This helps to evaluate the metabolic profile, plasma concentration, bio-availability etc of the formulation or chemical moieties under development “Pharmacokinetics”.

  • In plant constituents, there are many molecules with similarity in chemistry like isoflavones, glycosides, saponins etc. but different activity or nutritional value. These compound can’t be precisely determined by other methods, hence they are determined by LC-MS/MS analysis by means of separation into individual components and there by identification.

  • Qualitative analysis - Separation of chemical and biological compounds, e.g., drugs (aspirin and ibuprofen), proteins (egg white or blood), organic chemicals, herbal medicines and plant extracts.

  • Quantitative analysis - To determine the concentration of a compound in a sample by measuring the height and area of the chromatographic peak.

CCHE-57357 helps the community by providing exceptional services and solutions for them. Utilizing our sensitive mass spectrometry, a definite and accurate result is achieved to check product adulteration, detecting drug traces in urine sample and checking pesticide levels in food products.


Environmental Applications

  1. Detection of phenolic compounds in drinking water.
  2. Bio-monitoring of pollutants.

Applications in Forensics

  1. Quantification of drugs in biological samples.
  2. Identification of steroids in blood, urine etc.
  3. Determination of cocaine and other drugs of abuse in blood, urine etc.

Food and Flavor

  1. Measurement of Quality of soft drinks and water.
  2. Sugar analysis in fruit juices.
  3. Analysis of polycyclic compounds in vegetables.
  4. Preservative and insecticides analysis.

Applications in Clinical Tests and research

  1. Urine analysis, antibiotics analysis in blood, and detecting concentrations of potential clinical candidates like anti-fungal and asthma drugs.
  2. Analysis of bilirubin, biliverdin in hepatic disorders.
  3. Detection of endogenous Neuropeptides in extracellular fluid of brain etc.