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Analysis of Lysosomal Proteins in Complex Samples

Background of Lysosomal Proteins in Complex Samples Analysis

The number of proteins located within or on lysosomal membranes may far exceed the number of proteins verified experimentally to date. In addition, lysosomes can vary between cell types. To be able to assess these differences globally, an unbiased large-scale mass spectrometry-based proteomics approach plays a key role, which is usually done in the lysosome-enriched fraction. However, methods that enrich for lysosomes all require millions of cells or milligrams of tissue as starting material and do not include samples with low levels in these analyses. In addition, most lysosomal storage diseases (LSDs) can only be simulated in animal models, and it is often not possible to obtain sufficient numbers of lysosome-enriched fractions to hinder proteomic studies of LSDs.

Fig. 1. Workflow for sample preparation and analysis for lysosomal proteome analysis in complex samples. (Mosen P, et al., 2021)Fig. 1. Workflow for sample preparation and analysis for lysosomal proteome analysis in complex samples. (Mosen P, et al., 2021)

Our Lysosomal Proteins in Complex Samples Analysis Services

An alternative approach to identify lysosomal proteins from a small number of complex samples is a targeted proteomics strategy. To address the limitations of non-targeted data-dependent acquisition (DDA)-based strategies for acquiring lysosomal proteins, CD BioSciences developed targeted proteomics strategies to identify lysosomal proteins in complex samples. In addition, since the analysis of patient samples is limited by availability, sample type and conditions, we can also targeted analyze your lysosomal proteins of interest in clinical samples by adopting this strategy.

Our goal is to analyze the lysosomal proteome in samples of varying complexity for our global customers. Here, we develop the following two effective targeted proteomics strategies to provide lysosomal proteomic analysis services in complex samples. Our team will consider the advantages and disadvantages of both strategies to develop the best solution for you.

  • Parallel Reaction Monitoring (PRM)
    We use PRM techniques to fragment highly abundant peptides. This method is mostly used to study selected lysosomal proteins.
  • More proteins can be identified in less complex samples.
  • The gradient is longer.
  • Not limited by a predefined list of proteomic peptides.
  • PRM shows better performance in liver lysates, allowing the detection of quantitative changes not recognized by DIA.
  • Allows direct analysis of the lysosomal proteome from small amounts of whole tissue samples without the need for lysosomal enrichment.
  • Data Independent Acquisition (DIA)
    We perform unbiased slicing of predetermined m/z windows and identify the abundance of the respective peptides from unique fragment ions identified in the mixed MS/MS spectra for identification. This method is mostly used for the analysis of the entire lysosomal proteome.
  • More proteins can be identified in less complex samples.
  • Longer gradients.
  • Not limited by a predefined list of proteomic peptides.
  • No analytical development required, saving time.

Advantages of Our Targeted Proteomics Strategies

PRM and DIA methods are ideal for the analysis of lysosomal proteins from cellular or tissue samples with low abundance of peptides compared to DDA-based label-free quantification strategies.

  • Higher sensitivity.
  • Higher reproducibility.
  • No prior enrichment required.
  • Suitable for analysis of lysosomal proteins in all types.
  • Not suitable for samples of higher complexity, such as whole cell lysates.

CD BioSciences can meet any reasonable needs of our clients, taking time and budget into consideration for you. Our aim is to be customer-centric and to provide the highest quality services to customers. Our customer service representatives are enthusiastic and trustworthy 24 hours a day, 7 days a week. If you are interested in our services, please feel free to contact us for more information or a detailed discussion.

References

  1. Mosen P, Sanner A, Singh J, et al. (2021) Targeted quantification of the lysosomal proteome in complex samples[J]. Proteomes. 9(1): 4.
  2. Sleat D E, Ding L, Wang S, et al. (2009) Mass spectrometry-based protein profiling to determine the cause of lysosomal storage diseases of unknown etiology[J]. Molecular & Cellular Proteomics. 8(7): 1708-1718.

For research use only, not intended for any clinical use.

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