Proteomic analysis pipeline

In silico proteome analysis for biomarker identification aiding accelerated drug discovery for precision medicine

Biomarker identification is crucial for novel drug discovery and development. Proteomics is a powerful biomarker detection and identification technique through proteome characterization and assessment. We integrate the latest technological developments and statistical tools to facilitate quick and accurate biomarker identification. Our multidisciplinary teams leverage their experience and expertise in data sciences, biology, and chemistry to develop high-throughput solutions for biomarker detection.

Our Proteomics analysis offering includes the following:

End-to-end Biomarker detection pipeline

On-demand customizable Biomarker detection services


Key components of our Proteomics service:

Processing proteomics data

From mass spectrometry data sets using either TPP Pipelines or MaxQuant or from plasma proteins using affinity-based assays like high-throughput Olink Proximity Extension Assay

Data quality control

Detection and elimination of general and non-specific protein contamination and making protein abundance samples comparable and reliable through normalization to correct for bias

Differential analysis

Analysis and comparison of distinct proteomes in different conditions: healthy vs. diseased samples or pre vs. post-treatment samples

Enrichment analysis

Identifying specific functional pathways, biological processes, and cellular locations affected/involved in a particular disease or response mechanism

GWAS integration

Integrating proteomic analyses with GWAS results to identify genome variants and their functional correlation in the organism’s proteome
Given the data from the mass spectrometry process, the steps in the proteomics pipeline are protein identification and qualification; data cleaning, normalization and visualization; and downstream analysis. The data cleaning and visualization steps consist of generating heat maps, MA plots, and Volcano plots. Some of the reports generated in Downstream analysis include co-expression profiles, network inference, machine learning, and enrichment analysis among others.
Proteomics Pipeline


Researchers have unique needs based on research study, therapeutic modality focus, and disease area. As a service provider, we realize the need for more than a standard pipeline. We provide end-to-end services for the proteomics analysis customizable as per the user-defined problem statement. Details of our data processing and data quality control services are as below:

Data Procesing

Using inputs from mass spectrometry datasets or plasma proteins

TPP Pipelines

Open-source mass spectrometric data processing pipeline for protein assignment, quantification, and validation using TPP Petunia GUI or command-line interface scripts


End-to-end solution using mass spectrometry datasets as inputs and providing various output tables like level of protein groups, peptide-serum matches, and peptides

Affinity-based assays

Using plasma serum data to link protein-specific antibodies to DNA-encoded tags to research diverse biological processes

Data Quality Control

Essential for sound research and robust downstream analysis

Data Cleaning

Removal of non-protein molecules or peptides as well as low-quality and ambiguous samples. Use of Imputation methods to fill in missing values and data integration to combine dataset from multiple sources resulting in increased statistical power and more profound insights

Data Filtering

Large-scale mass spectrometry datasets transformed into more trustworthy and accurate proteome information using pre and post-filtering database search tools

Data Visualization

Analysis and interpretation of data using scatter plots, heatmaps, and volcano plots to explore relationships between proteins, highlight differences between experimental groups, and identify potential biomarkers or pathways that may be significant for further research


Accounting for bias to make samples more comparable using various regression techniques to ensure reliable downstream analysis and results

Discover our offerings across the biopharma value chain

Learn more about our Proteomic analysis pipeline