MtoZ Biolabs Empowers Research with High-Throughput Shotgun Proteomics Analysis

MtoZ Biolabs offers High-throughput Shotgun proteomics and advanced bioinformatics for diverse research needs.

BOSTON, MA, UNITED STATES, September 3, 2025 /EINPresswire.com/ -- Proteomics has emerged as a critical discipline for elucidating biological mechanisms, exploring disease pathogenesis, and accelerating drug discovery. With rapid advances in mass spectrometry(MS) and bioinformatics, proteomics has evolved from qualitative descriptions to quantitative analysis, and from single-target studies to system-wide investigations. Researchers increasingly seek to obtain comprehensive protein information within a single experiment to gain a holistic understanding of biological systems. However, challenges such as complex sample preparation, limited throughput, and incomplete data coverage continue to constrain deeper scientific insights.



Within this context, Shotgun proteomics has become a mainstream analytical strategy, offering high throughput, broad proteome coverage, and adaptability to diverse study designs. MtoZ Biolabs leverages advanced mass spectrometry platforms and a dedicated scientific team to deliver high-throughput Shotgun proteomics analysis solution. These integrated workflows help researchers overcome experimental bottlenecks and accelerate meaningful scientific outcomes.



Technological Innovation: Shotgun Technology for Large-Scale Protein Identification and Quantification

Shotgun proteomics represents a cornerstone methodology for large-scale protein identification and quantification. The approach involves enzymatically digesting proteins into peptides, separating them via liquid chromatography (LC), and subjecting them to high-resolution tandem mass spectrometry (MS/MS). Protein identity and abundance are subsequently inferred through database searching. Unlike targeted methods, Shotgun proteomics requires no predefined protein list and enables unbiased, discovery-driven investigations.

MtoZ Biolabs has advanced the field through several key enhancements:

●  Employing Nano-LC–HRMS platforms such as the Thermo Scientific Orbitrap Fusion Lumos and Q Exactive HF-X, ensuring efficient peptide separation and accurate mass detection;

●  Developing tailored sample preparation workflows optimized for a variety of specimens, including animal tissues, plant material, microbial samples, plasma, urine, and cerebrospinal fluid, thereby improving protein extraction and digestion efficiency;

●  Supporting both label-free quantification (LFQ) and multiplexed labeling approaches (TMT/iTRAQ) to provide flexibility for diverse experimental designs, enabling analysis of differential protein expression across groups and time points.



These advances position MtoZ Biolabs’ Shotgun proteomics at the forefront of global research standards, delivering broad coverage, high sensitivity, and robust stability for applications ranging from basic science to disease mechanism studies and drug research.



Workflow of Shotgun Proteomics Analysis

MtoZ Biolabs applies a highly standardized workflow to ensure reproducibility and reliability across Shotgun proteomics projects. Key steps include:

1. Protein Digestion

Complex protein mixtures are enzymatically cleaved using proteases such as trypsin. This process converts intact proteins, which are difficult to analyze directly by MS, into smaller peptides that are more readily detected, thereby increasing sensitivity and efficiency.



2. Peptide Separation

The resulting peptide mixture is resolved by HPLC or Nano-LC based on physicochemical properties such as hydrophobicity and charge. High-resolution separation minimizes signal overlap and ensures accuracy in downstream MS analysis.



3. Mass Spectrometry Detection (MS/MS)

High-resolution instruments (e.g., Orbitrap, Q-TOF) first conduct MS1 scans to determine peptide mass-to-charge ratios. Selected peptides are then fragmented in MS/MS analysis to generate characteristic ion spectra, enabling large-scale peptide profiling.



4. Database Searching and Quantification

Peptide matches are validated with a target–decoy database strategy at a 1% FDR, ensuring reliable protein sequence identification. Quantification is achieved using LFQ or TMT-based workflows. Post-translational modifications (e.g., phosphorylation, acetylation, ubiquitination) can also be characterized when combined with appropriate enrichment methods.



5. Functional Annotation and Biological Interpretation

Differentially expressed proteins undergo bioinformatics-driven interpretation, including GO annotation, KEGG pathway enrichment, and protein interaction network mapping. These analyses distill large datasets into biologically meaningful insights.



Four Core Advantages: Empowering Diverse Research Applications

MtoZ Biolabs’ high-throughput Shotgun proteomics analysis integrates technological refinement, customized design, stringent data quality control, and flexible delivery models to support a wide range of scientific needs.

1. High Coverage and Sensitivity

Many critical regulatory proteins exist at low abundance, posing detection challenges. Optimized separation strategies and advanced MS acquisition parameters, combined with high-resolution platforms, improve sensitivity to low-abundance signals, enabling comprehensive proteome profiling.



2. High Throughput and Tailored Workflows

The platform accommodates large-scale studies, cross-omics integration, and clinical applications. Workflows can be customized for specific objectives, including PTM characterization (phosphorylation, acetylation, ubiquitination) or complex sample matrices (e.g., plant cell walls, microbial membranes), ensuring adaptability to diverse research scenarios.



3. Comprehensive Quality Control and Multi-Layered Data Analysis

A robust QC framework spans sample receipt, preparation, MS acquisition, and data analysis. Standard peptides are used to monitor digestion efficiency, QC samples assess instrument performance, and strict FDR thresholds are applied. Multi-dimensional data interpretation—including differential protein profiling, GO/KEGG enrichment, and network analyses—ensures reliable and reproducible insights.



4. Flexible Delivery and Cost Efficiency

By streamlining sample processing and data analysis, MtoZ Biolabs delivers timely results while optimizing project costs. Services accommodate both exploratory and large-scale projects, with options for accelerated timelines to meet urgent research demands.



Application of Shotgun Proteomics Analysis

As an unbiased and comprehensive approach, Shotgun proteomics is widely applied across diverse scientific disciplines. Its capacity for broad detection and adaptable workflows makes it invaluable for basic discovery, medical research, agriculture, environmental science, and drug development.

1. Disease Mechanism Studies

Comparative proteomics identifies disease-associated proteins, informing mechanistic insights and therapeutic target discovery, particularly in oncology.



2. Biomarker Discovery

Large-scale protein profiling of plasma, urine, or cerebrospinal fluid enables biomarker identification using advanced statistical and machine learning approaches.



3. Drug Mechanism of Action Analysis

Pre/post-treatment proteomic comparisons elucidate pharmacodynamic pathways and off-target effects.



4. Environmental and Agricultural Sciences

Shotgun proteomics analysis applied to microbial diversity, plant/animal stress responses, and food safety testing to support environmental stewardship and sustainable agriculture.



What Could Be Included in Our Shotgun Proteomics Analysis Report?

1. Comprehensive Experimental Details

2. Materials, Instruments, and Methods

3. Total Ion Chromatogram & Quality Control Assessment (project-dependent)

4. Data Analysis, Preprocessing, and Estimation (project-dependent)

5. Bioinformatics Analysis

6. Raw Data



MtoZ Biolabs remains committed to its mission of driving scientific innovation and advancing life sciences, continually enhancing its technology portfolio. Future directions include exploring the integration of high-throughput Shotgun proteomics with single-cell proteomics and spatial proteomics, aiming to deliver next-generation solutions that accelerate scientific discovery. In an era where proteomics research is moving toward large-scale, high-precision, and multi-dimensional analysis, MtoZ Biolabs’ high-throughput Shotgun proteomics analysis provides comprehensive, reliable, and scalable analytical capabilities. It supports basic mechanistic studies, clinical biomarker discovery, and drug target validation with consistent rigor and efficiency.



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.


Media Contact

Name: Prime Jones

Company: MtoZ Biolabs

Email: marketing@mtoz-biolabs.com

Phone: +1-857-362-9535

Address: 155 Federal Street, Suite 700, Boston, MA 02110, USA

Country: United States

Website: https://www.mtoz-biolabs.com

Prime Jones
MtoZ Biolabs
+1 857-362-9535
marketing@mtoz-biolabs.com
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