Absolute Quantitative Analysis (AQUA) Service

What Is AQUA Absolute Quantification?

AQUA, or Absolute QUAntification, is a targeted mass spectrometry strategy that uses a stable isotope-labeled peptide corresponding to a predefined endogenous peptide as an internal reference.

This makes AQUA fundamentally different from routine relative proteomics. DIA, label-free, or conventional PRM comparison can show whether a target increases or decreases between samples; AQUA is designed to answer a different question: How much of this predefined protein or peptide is actually present in the sample?

When This Service Is a Good Fit

AQUA is therefore well suited to biomarker verification, absolute protein abundance measurement, batch or process comparison, targeted biological studies, and projects requiring concentration values that are more directly comparable than relative signal intensities.

Research Need	Recommended Approach
Determine the actual concentration of a specific protein	AQUA Absolute Quantification
Confirm the absolute concentration of a candidate biomarker	AQUA + PRM
Compare absolute concentrations across samples or batches	AQUA + Calibration Curve
Quantify a small panel of predefined proteins with high specificity	Multiplex AQUA / Targeted LC-MS/MS
Quantify a predefined endogenous peptide	Peptide AQUA Quantification
Quantify a phosphorylation, acetylation, or other modified peptide	Modified AQUA Peptide, subject to project-specific evaluation
Screen broadly for unknown differential proteins	Discovery proteomics such as DDA or DIA, followed by AQUA if absolute validation is required

AQUA Service at MtoZ Biolabs

MtoZ Biolabs provides AQUA-based protein absolute quantification services integrating protein preparation, targeted LC-MS/MS detection, and quantitative data analysis.

Our workflow includes:

• Target protein identification by LC-MS/MS
• Signature peptide evaluation and selection
• Stable isotope-labeled peptide standard design
• PRM-based targeted quantification
• Standard curve establishment
• Skyline-based quantitative analysis
• Absolute concentration calculation

For PRM-based AQUA projects, samples are processed through protein extraction, reduction and alkylation, enzymatic digestion, peptide purification, LC-MS/MS detection, and targeted data analysis.

In representative workflows, protein samples are processed using SP3-based peptide preparation, followed by Trypsin/Lys-C digestion and C18 desalting before LC-MS/MS analysis. The generated raw files are processed using targeted analysis software, where selected fragment ions are integrated for quantitative calculation.

AQUA Service Workflow

Experimental Instruments

MtoZ Biolabs applies high-resolution LC-MS/MS platforms for AQUA analysis, including:

Platform	Application
Orbitrap Exploris 480	High-resolution LC-MS/MS acquisition for targeted protein quantification
Vanquish Neo UHPLC System	Nano-flow liquid chromatography separation
Nano-LC system	Peptide separation before mass spectrometry detection

Typical LC-MS/MS workflows include:

• C18 reverse-phase chromatography separation
• Nano-flow LC operation
• High-resolution MS/MS acquisition
• Targeted PRM detection

Why Choose MtoZ Biolabs?

1.Integrated Protein Identification and Absolute Quantification Workflow

MtoZ Biolabs combines discovery-level protein identification with targeted AQUA quantification, helping researchers move from candidate discovery to accurate measurement.

2.High-Resolution LC-MS/MS-Based Quantification

High-resolution Orbitrap platforms provide accurate precursor and fragment ion measurement for targeted peptide detection.

3.Targeted PRM Quantification Strategy

PRM acquisition enables simultaneous monitoring of selected peptides with high specificity and detailed MS/MS information.

4.Comprehensive Quantitative Analysis

The workflow provides not only quantitative values but also supporting evidence including:

• Target peptide information
• MS detection results
• Standard curve evaluation
• Quantitative calculation records

5.Customized Quantification Strategies

AQUA workflows can be adjusted according to:

• Target protein abundance
• Sample complexity
• Quantification objectives
• Required sensitivity

Sample Submission Requirements

AQUA analysis can be developed for a range of biological matrices, including:

cell lysates, tissue lysates, plasma, serum, cerebrospinal fluid, urine, and other compatible biological fluids or protein solutions.

There is generally no intrinsic species restriction when the target sequence is known and a suitable signature peptide can be established.

Requirement	General Recommendation
Protein Amount	>50 μg total protein for routine protein-solution projects
Protein Concentration	>0.5 μg/μL recommended
Sample Format	Protein solution or other project-approved matrix
Preferred Buffer	Water, PBS, or MS-compatible low-interference buffer
Shipping	Frozen samples shipped on dry ice
Avoid Where Possible	High concentrations of detergents, especially SDS, and excessive salt

What Could Be Included in the Report?

The final AQUA report is designed to give you both the absolute quantitative result and the supporting data needed to evaluate and use that result in your study.

• Absolute concentration of the target protein or peptide
• Quantitative results for each submitted sample
• Calibration curve and quantitative performance information
• Target peptide and internal-standard signal comparison
• Supporting LC-MS/MS data for target confirmation
• Structured result tables for downstream comparison and interpretation
• Raw mass spectrometry data and a technical report

Start Your AQUA Project with MtoZ Biolabs

If you already have a target protein or peptide list, send us the target name or sequence, species, sample type, sample number, and expected quantitative range if known. Our team can evaluate signature peptide suitability, sample requirements, internal-standard strategy, and the appropriate targeted LC-MS/MS workflow before the project begins.

For projects where the quantitative strategy has not yet been finalized, we can also help determine whether relative PRM/MRM, AQUA absolute quantification, or a broader DIA-based workflow better matches the study objective.

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

Related Services

Targeted Proteomics Service

Peptide Absolute Quantification Service

Isotope Labeling-Based Quantitative Service

Quantitative Proteomics Service