Protein Quantification Analysis Service

Protein quantification is a crucial technique in proteomics research. By studying changes in protein expression levels under various conditions based on protein identification, it helps researchers discover new biomarkers or drug targets, contributing to early disease screening and prevention, disease monitoring, and treatment. Currently, protein quantification analysis service relies on high-throughput mass spectrometry, enabling the simultaneous detection of expression levels for thousands of proteins. Protein quantification can be categorized from different perspectives: by quantification method into relative quantification and absolute quantification, by experimental approach into labeled and label-free quantification, and by mass spectrometry acquisition mode into data-dependent acquisition (DDA) quantification and data-independent acquisition (DIA) quantification. These distinctions have given rise to a variety of protein quantification analysis service and sequencing strategies.

 



Figure 1. Protein Quantitative Omics.

 

Services at MtoZ Biolabs

MtoZ Biolabs provides a variety of protein quantification and sequencing strategies, offering precise protein quantification analysis service and subsequent data mining solutions. These include:

 

1. Protein Quantification Analysis Service Based on Wet Lab Experiments

In earlier studies, researchers widely adopted label-free detection methods. This approach involves extracting total protein from samples, digesting it into peptides, and subjecting the peptides to mass spectrometry to analyze their mass-to-charge ratios, ion intensities, and retention times. The characteristics and intensities of the proteins are then interpreted using database search software. The protein quantitative analysis service based on Label Free is simple to operate and low-cost, but the way each sample is processed separately will be interfered by human operations and instrument fluctuations, causing errors in the experiment.

 

As research projects expanded and sample sizes increased, AB Corporation introduced the iTRAQ isotopic tagging method. This approach labels each sample with a different isotopic tag at the peptide level, enabling qualitative and quantitative analysis by distinguishing isotopes in tandem mass spectrometry. The iTRAQ technique effectively minimizes variability caused by operators and instrument fluctuations, providing higher sensitivity and accuracy in protein quantification. Furthermore, it supports the simultaneous analysis of up to 8 samples per batch.

 

Later, Thermo also launched a TMT reagent kit, so that the protein quantitative analysis service can currently support up to 32 samples for testing in the same batch. Although isotopic-labeled quantification provides deeper detection, the cost of isotopic tags is significant. Additionally, due to the reagent's mechanism, this approach is only suitable for detecting the same region within the same species, limiting its application for comparing the presence or absence of proteins.

 



Figure 2. (A) Lable Free Experimental Flow (B) iTRAQ Experimental Flow (C) TMT Experimental Flow.

 

2. Protein Quantification Analysis Service Based on Mass Spectrometry Acquisition Modes

The above-mentioned protein quantitative analysis service primarily uses data-dependent acquisition (DDA) mode. In this mode, peptide fragments are injected into the mass spectrometer, which first collects primary parent ion data. The instrument then evaluates the intensity of parent ions and selects the top 20 or 40 ions for fragmentation in the collision cell. These secondary ions are subsequently detected. While this approach provides high-quality fragment ions due to its narrow acquisition window and strong ion intensity, it often misses low-abundance proteins due to its intensity threshold. To address this limitation, data-independent acquisition (DIA) mode was developed. Unlike DDA, DIA divides the parent ion acquisition window into multiple smaller windows and collects all parent ions indiscriminately in batches. This significantly reduces the loss of low-abundance proteins and offers higher stability and reproducibility, making it ideal for large cohort studies.

 

3. Protein Quantification Analysis Service Based on Quantification Methods

Protein quantification analysis service can be categorized into relative quantification and absolute quantification. Common methods like label-free, TMT, and iTRAQ belong to relative quantification. These techniques quantify the intensity of peaks on the spectrum to assign a value to peptides and proteins. However, the intensity does not directly reflect the actual expression level of a specific protein in the sample since the intensity is unitless. Relative quantification focuses on the ratio of intensities between experimental groups, identifying differences but without providing absolute quantities. Absolute quantification services, such as PRM targeted protein quantification, involve adding a fixed-mass internal standard during mass spectrometry analysis. By calculating the intensity ratio between the internal standard and detected substances, the absolute quantity of the target substance can be determined. This technique is primarily used for verifying specific proteins identified in untargeted proteomics experiments.

 

In addition to protein quantification techniques, proteomics research encompasses protein identification, post-translational modifications, subcellular localization, and subsequent experimental validations such as molecular biology techniques (e.g., CO-IP, WB). MtoZ Biolabs provides all these services.

 

Service Advantages

1. Advanced Analytical Platforms

MtoZ Biolabs is equipped with state-of-the-art mass spectrometry platforms, including 480, Astral, and TimsTOF high-resolution instruments, ensuring precise data for our clients.

 

2. Transparent Pricing

Our pricing is transparent, with no hidden  or additional fees.

 

3. High Data Quality

We utilize optimized experimental protocols to deliver superior-quality proteomics data. Comprehensive bioinformatics analysis ensures detailed data reports and visualizations.

 

4. Customized Research Solutions

MtoZ Biolabs offers tailored services based on your sample and research requirements, supported by expert consultation.

 

Sample Submission Suggestions

1. Sample Types

We accept multiple dimensions of sample types, including different animal and plant samples (cells, tissues, body fluids, etc.).

 

2. Sufficient Sample Quantity

 

Note: Except for FFPE samples, which are shipped at room temperature, all other samples are shipped on dry ice. The standard for sample delivery is the routine experimental process. If there are insufficient samples or other sample types, please contact technical personnel for free consultation.

 

Deliverables

MtoZ Biolabs offers not only accurate protein quantification analysis service but also premium post-analysis support. For protein quantification analysis service, we provide the following deliverables:

 

1. Comprehensive project report

 

2. Detailed experimental procedures

 

3. Materials, instruments, and method parameters

 

4. Total ion chromatograms

 

5. Data quality assessments

 

6. Bioinformatics analysis

 

7. Raw data files

 

The above constitutes the standard deliverables. Customized analysis can be evaluated based on specific requirements.

 

MtoZ Biolabs, an integrated Chromatography and Mass Spectrometry (MS) Services Provider, provides advanced proteomics, metabolomics, and biopharmaceutical analysis services to researchers in biochemistry, biotechnology, and biopharmaceutical fields. Our ultimate aim is to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample consumption. Free project evaluation, welcome to learn more details!