Quantitative Proteomics

Quantitative Proteomics

Quantitative Proteomics

Quantitative proteomics can be used to determine the relative or absolute amounts of proteins in your samples. For relative comparisons, label-free and chemical labelling approaches can be used. For absolute quantitation, stable isotope standards are used with techniques such as Selected Reaction Monitoring (SRM) or Parallel Reaction Monitoring (PRM).

At APAF, we provide quantitative proteomic services capable of assessing protein alterations in a wide variety of research contexts. Common examples include the assessment of protein expression changes in body fluids, cells, tissue, microorganisms, and plants.

Selected Services

Relative Quantitation: SWATH
SWATH is a relative quantitation approach which is well suited to large scale proteomic projects (tens to hundreds of samples).APAF offers SWATH services using nanoflow LC which provides superior sensitivity and concentration-response outcomes for your project. SWATH is well suited to most protein sample types including cells, tissue, biofluids, bacteria, fungi, and plants. APAF has recently developed bioinformatics tools to enhance SWATH analysis using our own SWATH Extend approach.

Chemical Labelling and Sample Multiplexing: Tandem Mass tags
The multiplexed nature of Tandem Mass Tags (TMT) provides an efficient and cost-effective approach for quantitative proteomic projects. When combined with sample fractionation using high pH offline reverse-phase HPLC, TMT quantitation provides in depth sample analysis and differential expression profiling. TMT can be used for larger sample numbers, and is well suited to cell culture studies, microbiological applications, and plant based studies. APAF has recently established 10plex-TMT protocols for organelle profiling, including exosomes and microparticles, phosphorylation studies, and for depleted and undepleted plasma proteomic studies.

Targeted Quantitation: SRM, PRM and MRM-HR
Targeted mass spectrometry approaches such as Selected Reaction Monitoring (SRM), Parallel reaction Monitoring (PRM) and Multiple Reaction Monitoring – High Resolution (MRM-HR) are are used for the specific quantitation of a smaller numbers of target proteins in complex samples. Targeted approaches yield improved sensitivity, specificity and reproducibility, and are commonly used in conjunction with stable isotope standards for the absolute quantitation of target proteins. APAF uses Q-tof, orbitrap, and Q-trap technology for targeted quantitative studies using SRM, PRM, or MRM-HR.

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