Proteomics and Mass Spectrometry Services

Proteomics is the study of structure and functions of proteins. The past decade has seen massive improvements in the field of proteomics and the depth of sampling has improved tremendously. Liquid chromatography coupled to mass spectrometry (LC- MS/MS) has become the backbone for proteomics for understanding biochemical pathways and  discover new biomarkers for debilitating diseases like cancer. ITSI Biosciences offers proteomics services utilizing advanced LC-MS/MS technologies to provide unsurpassed protein identification, quantitation and characterization services for more than 8 years. The proteomics services are offered to both industrial and university clients at a competitive price and faster turnaround time.

We utilize state of the art techniques and constantly update our skills and equipment to accommodate the constantly evolving proteomics field.  Our standard proteomics and mass spectrometry services will include some or all of the following steps (The list below is just for reference and is not exhaustive. Please don't hesitate to call us for techniques not listed here).

Experimental Design:
ITSI – Biosciences will work with clients to design experiments free of charge. With over 20 years combined experience, ITSI – Bioscience scientists will help design experiments to ensure that adequate number of samples are used, to ensure sufficient balance and statistical power.     

Sample preparation and qualification:
For a small fee, ITSI – Biosciences will help with sample preparation and qualification prior to the proteomics step. By having us prepare your samples the client is assured that all stringent quality control parameters are met before  movingon to the more expensive proteomics steps, thereby saving time and money. 

In-gel Digestion:
Gel Electrophoresis provides the reproducible, affordable and reliable way to fractionate proteins based on molecular weight or in combination with pI to reduce sample complexity at the protein level. Our in-gel digestion proteomics workflow includes spot picking, digestion and mass spec analysis from SDS-PAGE 1D gels,  2D-PAGE gels and 2D-DIGEgels.

In solution / Gel Free  Digest
Un-fractionated or fractionated proteomics samples such as those from online protein fractionation can be directly digested using trypsin or other proteases including aspN, Glu-C, and ArgC. This approach eliminates time consuming SDS-PAGE and also reduces the loss associated with protein recovery during in-gel digestion. We have expertise to optimize nano-LCMS for working with tryptic peptides and also with non-tryptic peptides including naturally occurring peptides - e.g. from cerebrospinal fluid.

Phosphopeptide identification
Identifying proteins is the first proteomics step and identifying post translational modifications including phosphorylation is prerequisite to assigning a role to the protein in a signaling pathway or in other biochemical pathways. We have extensive experience in method development for enriching phosphopeptide using either TiO2 or IMAC approach. Apart from TiO2  or IMAC approaches, we also have expertise for using SCX fractionation for phosphopeptide fractionation / enrichment.
Apart from the sample preparation and tryptic digestion services prior to proteomics,  we offer an innovative kit (ProDM – Cat #: K-0021-10) to check for completion of trypsin digestion without gel electrophoresis prior to mass spectrometry. This is valuable for clients mailing precious samples that don’t have the means or time to verify complete trypsin digestion. 
We also offer image analysis, spot detection, automated spot picking and robotic digestion from 2D-DIGE gels. We work with a variety of gel stains including Sypro Ruby, Coomassie blue, and fluorophores.

Biomarker Analysis:
Plasma / Serum Depletion:
We have both in-house validated albumin depletion kit (ASKc; Cat #K-0012-10 and ASKs; Cat #K-0013-50) and a 14 proteins depletion kit for depletion of abundant proteins from serum/plasma prior to analysis. Removing 14 most abundant proteins reduces plasma protein concentration by at least 90 %. Without depletion it is difficult to identify biomarkers which are usually in the low copy numbers compared to albumin or IgGs. Depleting them increases our ability to identify low abundant proteins and hence candidate biomarkers. 

As part of the biomarker discovery and analysis, we offer protein quantification using Isobaric Tags for Relative And Absolute Quantitation (iTRAQ) labeling.  We routinely employ 4 or 8-plex iTRAQ for identifying proteins that show differential expression in biopsies such as, urine, serum, plasma and other body fluids. 


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Important Info

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