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General Proteome

Product Introduction

General proteome is the study of proteomes, focusing on the composition of proteins in cells, tissues, or organisms and their patterns of variation. Essentially, proteomics refers to the study of proteins at a large scale, including their expression levels, post-translational modifications, and protein-protein interactions, providing a comprehensive understanding of processes such as disease development and cellular metabolism. Depending on the techniques used, conventional proteomics can be categorized into label-free proteomics, DIA proteomics, direct DIA proteomics, and TMT proteomics.

Product Features

Table Characteristics of various techniques in proteomics

Category	label-free	DIA	Direct DIA	TMT
Data Acquisition Mode	DDA	DIA (Detection) + DDA (Library Building)	DIA	DDA
Need for Labeling Reagents	No	No	No	Yes
Number of Identified Proteins	Few	Many	Many	Few
Quantitative Accuracy	Low	High	High	High
Reproducibility	Low, with many missing values	High	High	High
Quantitative Stability	Low	High, with few missing values	High, with few missing values	High, with few missing values
Identification Coverage	Low	High	High	High
Detection Sensitivity	Fast	High	High	High
Turnaround Time	Low	Slower	Fast	Slow
Cost	Small sample amount	High	Low	High
Recommended Sample Amount	No	Large sample amount	Small sample amount	Small sample amount

Protein Quantification Techniques

(1) Label-free

Label-free quantification technology for proteins is a method that utilizes liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze peptides derived from protein digestion. This approach does not require the use of expensive stable isotope labels as internal standards; instead, it directly analyzes the mass spectrometry data produced during large-scale protein identification. By comparing the signal intensities of corresponding peptides in different samples, relative quantification of the proteins corresponding to these peptides can be achieved.

Product Features

Isotope labeling, simple operation, and lower cost
Lower identification coverage and sensitivity
Requires high quality mass spectrometry equipment, with both chromatography and mass spectrometry needing good stability and reproducibility
Not limited by the number of samples
Enables "presence/absence" comparative analysis of proteins can be performed

(2) DIA

DIA technology primarily employs data-independent acquisition (DIA) mode and combines it with traditional data-dependent acquisition (DDA) mode to build a spectral library. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), the entire mass range of the MS scan is divided into several windows, and all ions within each window are sequentially fragmented, collecting information on all fragment ions. The obtained data can be analyzed using mainstream software for proteomics identification, quantification, and differential protein analysis. This technique does not require specifying target peptides and can comprehensively capture all fragment ion information from the sample, significantly enhancing data utilization.

Product Features

High identification sensitivity:Capable of identifying more low-abundance proteins, thereby enhancing the credibility of quantitative analysis.
Improved repeatability:Compared to DDA mode, DIA has fewer missing values and higher data consistency.
Data traceability:Digitized protein information allows for retrospective analysis.
Suitable for large sample sizes:Not limited by sample quantity, suitable for analyzing large numbers of samples.
High quantitative accuracy:Lower CV values, resulting in improved quantitative precision.

(3) Direct DIA

Direct DIA (direct data-independent acquisition) is a DIA technique that does not rely on spectral library construction. Unlike traditional DIA analysis strategies, Direct DIA does not involve DDA tiered library building but instead uses machine deep learning to generate spectral libraries directly from DIA raw files. Deep learning scoring is used to identify fragmentation patterns of spectra peaks, predict retention times, and remove false positive results. Compared to DDA, it has fewer missing values, identifies more proteins, and offers higher quantitative accuracy; compared to traditional DIA techniques, this significantly reduces costs and narrows the gap in the number of identified proteins.

Product Features

DIA full-scan provides good data integrity and high protein coverage.
No need for DDA library construction, improving efficiency and reducing experimental costs.
Fewer missing values, good reproducibility, and accurate quantification.

(4) TMT

TMT technology is a quantitative proteomics method based on the principle of chemical labeling, which enables simultaneous quantitative analysis of proteins across multiple samples. This technique uses specific chemical reagents (TMT labels) to tag proteins in different samples, giving them distinct mass-to-charge ratios, followed by quantitative analysis through tandem mass spectrometry (MS/MS).

Product Features

TMT technology enables simultaneous analysis of multiple samples, improving analytical efficiency.
TMT technology allows for the detection of low-abundance proteins.
TMT technology provides precise quantitative results, facilitating quantitative comparisons and trend analyses.

Experimental Process

Analysis Process

(1) DIA/Label-Free/Direct DIA

(2) TMT

Presentation of Analysis Results

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