AQUA Proteomics Service

What Is AQUA Proteomics?

AQUA (Absolute QUAntification) is a targeted LC-MS/MS approach for absolute protein and peptide quantification using stable isotope-labeled peptides. It is designed to determine the actual amount or concentration of predefined target proteins or peptides in biological samples.

 

AQUA quantification uses a proteotypic peptide from the target protein and a corresponding stable isotope-labeled heavy peptide as an internal standard. The heavy and endogenous light peptides behave similarly during LC-MS/MS but can be distinguished by their mass difference.

 

Using Orbitrap PRM, the Light/Heavy response ratio is measured and applied to a calibration curve generated from known standards to determine the absolute amount of the target peptide and corresponding protein.

Figure 1. Principle of AQUA Proteomics for Absolute Protein Quantification

When This Service Is a Good Fit

Research Need	How AQUA Helps
Determine the actual concentration of a specific protein	AQUA Absolute Quantification
Confirm the absolute concentration of a candidate biomarker	AQUA + PRM
Compare the absolute amount of a specific protein across samples or batches	AQUA + Calibration Curve
Perform highly specific absolute quantification of a small number of predefined targets	AQUA PRM
Quantify specific modified peptides, such as phosphorylated or acetylated peptides	Modified AQUA Peptide; project-specific evaluation required

Service at MtoZ Biolabs

MtoZ Biolabs provides customized AQUA absolute quantification services for studies with predefined target proteins that require actual protein or peptide amounts or concentrations. Projects can range from a single target to multi-protein panels, with AQUA-PRM strategies designed according to target number, sample matrix, expected abundance, and quantitative requirements.

 

For projects with predefined target peptides, stable isotope-labeled AQUA peptides can be designed based on the specified sequences. If only the target proteins have been identified and suitable quantitative peptides have not yet been selected, we can evaluate the protein sequences and recommend candidate proteotypic peptides for absolute quantification.

 

For studies involving multiple targets, MtoZ Biolabs can develop multi-protein quantitative panels according to the study design. For projects involving more than 20 target proteins, we evaluate sample number, target abundance, and throughput requirements to determine whether AQUA-PRM remains appropriate or whether a DIA strategy combined with stable isotope-labeled internal standards should be considered.

Analysis Workflow

1. Target & Peptide Selection  

Confirm target proteins and sample information and select proteotypic peptides suitable for absolute quantification.

 

2. AQUA Peptide Preparation  

Design and prepare stable isotope-labeled AQUA internal standard peptides with >95% purity.

 

3. Method & Calibration Development  

Establish and optimize the PRM method and generate a calibration curve using at least six concentration points.

 

4. Sample Preparation  

Perform sample preparation, protein digestion, and AQUA internal standard peptide addition.

 

5. PRM LC-MS/MS Analysis  

Analyze target peptides by PRM using high-resolution Orbitrap mass spectrometry.

 

6. Absolute Quantification & Reporting  

Calculate absolute concentrations based on endogenous/heavy peptide responses and the calibration curve, followed by quality control and reporting.

Why Choose MtoZ Biolabs?

1. High-Resolution Orbitrap PRM Analysis

Orbitrap high-resolution mass spectrometry with PRM acquisition provides selective and reliable detection of target peptides in complex biological samples.

 

2. Rigorous Calibration and Quality Control

Multi-point calibration curves are used for quantification and quality control, with calibration curve R² values >0.99 to support reliable linear response across the target concentration range.

 

3. Fmol-Level Quantification

AQUA-PRM methods can be optimized for low-abundance targets, with limits of quantification reaching the fmol level and supporting absolute quantification of low-abundance target proteins or peptides in complex samples.

Sample Submission Requirements

Item	Requirement
Sample Types	Cells, tissue lysates, plasma, serum, cerebrospinal fluid, urine, and other biological fluids
Species	No species restriction; the target protein sequence must be available
Minimum Protein Amount	>50 μg total protein in solution
Protein Concentration	>0.5 μg/μL
Recommended Buffer	Water or PBS
Storage & Shipping	Store frozen and ship on dry ice
Avoid	High concentrations of detergents or salts, SDS, and cross-linking reagents

Samples containing high concentrations of SDS or cross-linking reagents, as well as samples with severe protein degradation, may interfere with protein digestion and subsequent LC-MS/MS analysis. Lipemic plasma or serum and other samples with complex matrices should be evaluated before project initiation.

Deliverables

1. Absolute Concentration Table (Excel)

2. Calibration Curve

3. Raw Mass Spectrometry Files

4. Target Peptide Quantitative Data

5. PDF Technical Report

Data processing is primarily performed using Skyline. Protein sequence and peptide information can be referenced against the UniProt database, and custom protein sequence databases provided by clients are also supported.

FAQs

Q1: What is the difference between AQUA and PRM?

PRM is a targeted mass spectrometry data acquisition mode, whereas AQUA is an absolute quantification strategy. The MtoZ Biolabs AQUA workflow uses Orbitrap PRM for target peptide acquisition and stable isotope-labeled peptides as internal standards for absolute quantification.

 

Q2: Can AQUA analysis be performed if I know the target protein but have not selected a target peptide?

Yes. Clients can specify a heavy-labeled peptide directly, or MtoZ Biolabs can evaluate the target protein sequence and recommend candidate proteotypic peptides suitable for absolute quantification.

 

Q3: Can AQUA replace ELISA?

AQUA and ELISA use different detection principles. ELISA relies on target-specific antibodies, while AQUA uses target peptides and stable isotope-labeled internal standards for LC-MS/MS quantification. AQUA is particularly useful when suitable antibodies are unavailable or when mass spectrometry-based absolute quantification is required.

 

Contact Us

If your candidate proteins have already been identified and the next stage of your study requires actual absolute amounts rather than fold changes alone, submit your target list to MtoZ Biolabs for AQUA project evaluation.

 

MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.

Related Services

Absolute Quantitative Analysis (AQUA) Service

Peptide Absolute Quantification Service

Quantitative Proteomics Service

Quantification Mass Spectrometry Service