Label-Free Peptide Quantification Service

What Is Label-Free Peptide Quantification?

Label-Free Peptide Quantification uses LC-MS/MS for peptide identification and relative quantification. MS/MS fragment information is used to confirm peptide sequences, while chromatographic peak areas or mass spectrometric signal intensities of identified peptides are used to calculate relative abundance. The entire analysis does not require isotopic or chemical labeling.

 

Label-Free Peptide Quantification uses peptides as the final targets of quantification and mainly provides Peptide IDs, relative abundance, and differential peptide results. Peptide signals are not aggregated into protein abundance. If the research objective is protein-level quantification, Protein-Level Label-Free Quantitative Proteomics should be used.

 

Figure 1. Peptide-Level vs Protein-Level Quantification.

 

Services at MtoZ Biolabs

Based on a high-resolution liquid chromatography–tandem mass spectrometry (LC-MS/MS) platform, MtoZ Biolabs provides label-free peptide quantification services for relative quantification of peptides in different samples. The analysis does not require isotopic or chemical labeling; relative abundance is calculated from peptide mass spectrometric signal intensity or chromatographic peak area. MtoZ Biolabs can analyze serum, plasma, tissue, cell, and extracted peptide samples to obtain peptide identification, relative quantification, and differential peptide results, providing a data basis for subsequent candidate peptide screening and related functional studies.

When This Service Is a Good Fit

Label-Free Peptide Quantification is suitable for the following research needs:

• The research objective is to obtain peptide-level relative quantification results rather than global protein abundance.
• Relative peptide abundance needs to be compared among different experimental groups, treatment conditions, or time points.
• Differential peptides need to be screened as candidates for subsequent targeted validation or further research.
• The project requires label-free relative quantification without isotopic or chemical labeling.
• Peptides have already been extracted and require further LC-MS/MS identification and relative quantification.

 

Label-Free Peptide Quantification provides relative abundance results and does not directly provide absolute peptide concentrations. Absolute quantification or highly selective quantification of specific target peptides requires an appropriate absolute or targeted quantification strategy.

Analysis Workflow

1. Sample or Peptide Preparation

Extracted peptides undergo the necessary processing before LC-MS/MS analysis; biological samples such as serum, plasma, tissue, or cells first undergo appropriate peptide preparation.

 

2. LC-MS/MS Acquisition

After peptide separation by liquid chromatography, the mass spectrometry platform acquires MS and MS/MS data.

 

3. Peptide Identification

Peptide sequences are identified based on MS/MS fragment information.

 

4. Relative Quantification

Relative abundance is calculated from the chromatographic peak area or mass spectrometric signal intensity of identified peptides.

 

5. Differential Peptide Analysis

Relative peptide abundance is compared according to the experimental groups, and differential peptides are screened.

 

Why Choose MtoZ Biolabs?

1. High-Resolution LC-MS/MS Platform

MtoZ Biolabs uses high-resolution LC-MS/MS for peptide separation, identification, and relative quantification.

 

2. Peptide-Level Results

The main project outputs include Peptide IDs, relative abundance, and differential peptides, without confusion with protein-level LFQ results.

 

3. Multiple Sample Submission Formats

MtoZ Biolabs accepts extracted peptides and can also analyze serum, plasma, tissue homogenates, cell lysates, and other samples depending on project conditions.

 

4. Project Data Delivery

Projects can provide Peptide IDs, relative abundance, differential peptide results, analysis reports, and raw data.

Sample Submission Suggestions

Item	Suggestion
Extracted peptide samples	Maintain peptide integrity and sample quality, and minimize obvious protein contamination.
Biological samples that can be processed	Serum, plasma, tissue homogenates, cell lysates, etc.
Storage conditions	Store at -80°C.
Shipping conditions	Ship on dry ice and minimize repeated freeze-thaw cycles.
Project information	Provide sample type, peptide extraction status, group design, biological replicates, sample amount, and research objectives.

 

Sample type and peptide extraction status can affect sample preparation and LC-MS/MS analysis arrangements. For limited sample amounts, complex sample compositions, or samples in which peptide extraction has already been completed, sample information should be provided before submission so that the MtoZ Biolabs technical team can evaluate the sample conditions.

Applications

1. Differential Peptide Studies

Compare relative peptide abundance among treatment groups, time points, or experimental conditions and screen differential peptides.

 

2. Candidate Peptide Screening

Screen candidate peptides from differential peptide results for subsequent targeted validation or further research.

 

3. Treatment Response Studies

Compare changes in relative peptide abundance before and after drug treatment or other experimental treatments.

 

4. Time-Series and Group Comparisons

Compare relative peptide abundance at different time points or among experimental groups to observe peptide change trends.

 

5. Exploratory Peptide Quantification

Applicable to research projects requiring peptide identification, relative quantification, and differential peptide results.

 

Deliverables

 

FAQ

Q1: What is the difference between Label-Free Peptide Quantification and Protein-Level Label-Free Quantitative Proteomics?

Label-Free Peptide Quantification uses peptides as the final targets of quantification and provides peptide identification and relative quantification results. Protein-Level LFQ further aggregates peptide quantification information into protein abundance.

 

Q2: Can already extracted peptides be submitted directly?

Yes. Extracted peptides should maintain good sample quality and peptide integrity, with obvious protein contamination minimized. The extraction method, sample source, and storage conditions should be provided before sample submission.

 

Q3: Can conventional Label-Free Peptide Quantification be used directly for PTM peptide quantification?

Conventional Label-Free Peptide Quantification is mainly used for peptide identification and relative quantification. Quantification of modified peptides, such as phosphorylated or acetylated peptides, usually requires corresponding modified-peptide enrichment and dedicated analysis workflows.

 

Q4: What information should be provided before project consultation?

Sample type, whether peptide extraction has been completed, group design, biological replicates, sample amount, storage conditions, and research objectives should be provided so that the technical team can evaluate sample processing and the LC-MS/MS analysis plan.

 

MtoZ Biolabs provides Label-Free Peptide Quantification Service. For project consultation, sample type, peptide extraction status, group design, biological replicates, sample amount, and research objectives should be provided so that the MtoZ Biolabs technical team can evaluate sample processing and LC-MS/MS analysis arrangements.