Top-Down and Bottom-Up Proteomics Differences

Mass spectrometry-based top-down and bottom-up techniques are two common strategies in proteomics research. They differ significantly in detection principles, sample processing, instrument requirements, and applicable scope.

Top-down proteomics involves the analysis of intact proteins for quantification. Top-down does not require protein digestion and can directly proceed to mass spectrometry analysis. Its pretreatment process is simpler compared to bottom-up, maintaining better protein integrity and preserving more modification information. For individual proteins, top-down analysis can identify proteins and characterize post-translational modifications (PTMs). For protein complexes, this method can reveal combinations of protein complexes and their PTMs. However, compared to bottom-up proteomics, top-down has significant drawbacks in protein fractionation, ionization, and fragmentation. It is challenging to achieve gas-phase separation and has larger detection errors.

Bottom-up proteomics refers to qualitative and quantitative analysis of peptides resulting from protein digestion. The bottom-up analysis method based on protein mixtures is also known as the shot-gun method. In a typical bottom-up proteomics experiment, complex samples are enzymatically digested into peptides, which are then separated in one-dimensional or multi-dimensional chromatography steps before mass spectrometry analysis. Currently, proteomics research mainly employs the bottom-up strategy, as its detection results are accurate and amino acid sequences are easy to analyze. It is widely used for protein identification, characterization, and quantification. However, it has low sequence coverage and can only obtain partial information. There is a risk of peptide loss during sample preparation and digestion, and large regions of proteins may not be identified, leading to loss of information on PTMs and sequence variants.

Biotree Biotech uses the Thermo Fisher Orbitrap Fusion Lumos mass spectrometry platform combined with nanoLC-MS/MS nano-chromatography to provide top-down proteomics and bottom-up proteomics analysis services, including protein sequencing, PTM characterization, and protein structure characterization. You only need to inform us of your experimental objectives and send your samples. We will take care of all subsequent project matters, including cell culture, cell labeling, protein extraction, protein digestion, peptide separation, mass spectrometry analysis, raw data analysis, and bioinformatics analysis.

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