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The Proteomics and Metabolomics Program

Services and Costs

We offer a unique service with different assay length and applications. Our uniqueness stems from the fact that we are simply the only ones offering these services in Egypt. Costs include reagents, sample processing, manpower, instrument usage, data analysis and reporting.


General workflow

We work professionally according to world standards to ensure accurate, sensitive results. For all samples we perform an efficient protein extraction using varieties of extraction buffers, quantification of proteins and appropriate protein reduction and alkylation prior to trypsinization. All samples are subjected to C18 desalting step to make sure purified peptides are going to our clean TripleTOF 5600+.


Data analysis

  • Data is searched by up to two tandem mass spectrometry protein identification algorithms, including X!Tandem, OMSSA, comet, tide, andromeda.
  • Label free quantification based on spectral abundance “NSAF or emPAI” or area under the curve “AUC” is provided free of charge
  • Samples or groups of samples are compared, generating fold-change values for every measured protein.

Free (requires appointment)

  • Assay: (365 Proteome profiling)
  • Specifications: nanoLC-MS/MS, 10,000 sequencing events, 15 cm column, 20-30 min gradient.
  • Sample types: Affinity-purified samples or characterization of individual proteins
  • Assay: (365 Proteome profiling)
  • Specifications: nanoLC-MS/MS, 50,000 sequencing events, 15 cm column, 60 min gradient.
  • Sample types: sub-cellular fractions, exosomes, prokaryotic organisms
  • Assay: (365 Proteome profiling)
  • Specifications: nanoLC-MS/MS, 150,000 sequencing events, 15 cm column, 90 min gradient.
  • Assay: (365 Proteome profiling)
  • Specifications: nanoLC-MS/MS, 250,000 sequencing events, 15 cm column, 180 min gradient.
  • Sample types: Eukaryotic organisms, biofluid plasma/serum/urine/saliva profiling, host-pathogen profiling and microbiome profiling, and other samples consisting of a mixture of organisms.
  • Assay: (365 Proteome profiling- Library building)
  • Specifications: nanoLC-MS/MS, 450,000 sequencing events, 15 cm column, 180 min gradient in a replicates (3-5) until saturation.
  • Sample types: Ideal for building a comprehensive proteomic library of a single organism for maximum sequence coverage and post-translational modification characterization
  • Assay: (“Per- band/ Per lane” sequencing)
  • Specifications: nanoLC-MS/MS, 15 cm column, 30 min gradient per slice/band.
  • Sample types: Ideal for one dimensional and 2 dimensional electrophoresis
  • Assay: (Post-translational modification (PTM) analysis)
  • Specifications: nanoLC-MS/MS, 15 cm column, 60-120 min gradient depending on sample complexity.
  • Sample types: Ideal for one dimensional and 2 dimensional electrophoresis
  • Assay: (IP/MS analysis)
  • Specifications: nanoLC-MS/MS, 15 cm column, 60-120 min gradient depending on sample complexity.
  • Sample types: Antibody based capturing coupled with MS analysis
  • Assay: (relative quantification analysis)
  • Specifications: nanoLC-MS/MS, 15 cm column, 60-120 min gradient depending on sample complexity.
  • Sample types: SILAC for cell culturing and dimethyl- labeling works will most biological samples.
  • Assay: (MRM/SRM analysis)
  • Specifications: nanoLC-MS/MS, 15 cm column, pilot exploratory run followed by targeted 30- 60 min gradient.
  • Sample types: any biological sample.
  • Assay: (Plasma profiling)
  • Description: DDA (Data dependent acquisition method). The sample is depleted from highly abundant proteins such as albumin and globulin then subjected to Lc-MS/MS analysis.
  • Specifications: nanoLC-MS/MS, 15 cm column, 60-180 min gradient depending on sample complexity.
  • Sample types: plasma/ serum
  • Assay: (SWATH technology)
  • Description: DIA (Data independent acquisition method) that captures most peaks in the sample and searched against a library.
  • Specifications: nanoLC-MS/MS, 15 cm column, 60-180 min gradient depending on sample complexity.
  • Sample types: any biological sample/fluid
  • Assay: (Pharmaceutical and small molecule analysis)
  • Description: TDM, drug delivery, pharmacokinetics and other.
  • Specifications: Customized depending on experimental.
  • Sample types: any biological sample/tablets and other drug formats

The service provides three types of analysis:

  • Positive mode.
  • Negative mode.
  • Both modes; with a 30% reduction in the service cost.
  • Assay: (Adulteration, Forensic, Pesticide)
  • Description: testing adulteration in juice, detecting pesticide levels in food and checking drug residues in urine.
  • Specifications: Customized depending on experimental.
  • Sample types: any biological sample/tablets and other drug formats
  • Assay: (Comprehensive report “In-depth analysis”)
  • Specification: For Proteomics or metabolomics analysis, a set of comprehensive tests and software “see instruments and software tab” will be used to generate a ready publishable data and graphics. This utilize a set of bioinformatics data analysis software and R language. More details are available upon request.
  • Model Report
  • Model report (Proteomics)
  • Gene Ontology and enrichment analysis
  • Marker View
  • Peak View
  • Peptide Shaker
  • Peptide Shaker
  • Peptide Shaker
  • Protein pilot
  • Protein-pilot
  • Quality control analysis
  • Statistic analysis


    Confidentiality

    All identifying information about the samples' participants will be confidential and masked for subsequent usage. Confidentiality will be maintained including any limitations. The sample provider will be informed and acknowledged in any documents provided from these samples.



    Right to Refuse

    The samples provider may refuse to allow samples to be kept or put restrictions on those samples with no loss of benefits.


    Declaration of uncertainty

    Dear Customer,

    Although the Proteomics and metabolomics unit takes all precautions to produce an internationally standardized results and associated reports, in some cases, and due to the nature of the samples, we cannot guarantee the reproducibility and outcome of the results.

    This is simply due to the nature of the sample rather than any artifacts due to sample processing, mass spectrometric optimization.

    You are signing on this document to be noticed that our unit won’t bear responsibility of failure of analysis due to the nature of samples.

    Associated prove of optimized procedures is provided within this analysis will be delivered to you in case of analysis failure. In such case, please note that CCHE 57357 will not bear responsibility of reanalyzing the sample again and the unit have the right to reject further analysis of such sample(s) to keep our mass spectrometry clean and optimized.

    I Agree



    We regret to accept any service inquiries through phone calls. Instead, expect a reply to your email inquiry within 2 working days


    To be filled only after you have received an email from us that we have accepted your sample.


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    Consent form application tutorial:


    https://ptracking.57357.org