Bottom-Up Proteomics Analysis

Creative Proteomics offers a bottom-up proteomics approach based on biomass spectrometry analysis. Bottom-up, also known as shotgun, is a widely used mass spectrometry technique in proteomics research. It is the traditional method of hydrolyzing and enzymatically decomposing large protein fragments into peptides, which are then analyzed.

Bottom-up proteomics extracts proteins from cell or tissue lysates separates them by gel or LC and analyzes them directly by MS to provide a comprehensive view of all protein forms, including those with PTM and sequence variants. However, this method can only recover a small and variable fraction of the total peptide population of the protein, resulting in a low percentage coverage of the protein sequence. A lot of information about PTMs and alternatively spliced variants may be lost.

Fig. 1 The workflow in the bottom-up proteomics analysis. (Fredman, G, et al., 2022)

Service Content of Bottom-Up Proteomics Analysis

Bottom-up proteomics is the most established and widely used protein identification and characterization method. It applies to the study of all proteins in complex mixtures, such as serum, urine, and cell lysates. The primary approach is to identify proteins by enzymatic digestion of the mixture, followed by separation of the peptides by liquid chromatography (LC), followed by identification of the peptides using tandem mass spectrometry (MS/MS). This method is capable of identifying all the proteins of a sample, and hundreds of proteins can be determined simultaneously.

Mass Spectrometry Facilities and Projects

• Tandem Mass Spectrometry (MS/MS)
• 2D Gel Electrophoresis with MS/MS

Requirements for Samples

• We are able to accept almost all sample types.
• Please provide the specific concentration, volume, preparation time, and source of each sample. And inform the sample information as well as the control and experimental samples (if there is a group, describe the group information in detail.)

Deliverables

• Experimental steps
• Relevant mass spectrometry parameters
• Details of the identified phosphorylation sites
• Mass spectrometry images
• Raw data

Advantages of Bottom-Up Proteomics Analysis

• Can be applied to dynamic proteomics analysis.
• Enables comparative analysis of different samples.
• Ideal for protein biomarker discovery and research.
• Enables large-scale and global protein identification and quantification.

Service Process

Creative Proteomics, as an industry leader, is focused on providing you with a bottom-up proteomics analysis service based on mass spectrometry facilities. If this is of interest to you, please do not hesitate to contact us directly for a detailed discussion with our project experts.

Reference

1. Fredman, G.; et al. Towards Precision Dermatology: Emerging Role of Proteomic Analysis of the Skin. Dermatology. 2022, 238(2): 185-194.