⚠️ Common Pitfalls in Proteomics Projects:

• ❌ Unaddressed missing peptide intensities inflating false positives
• ❌ Batch effects overshadowing real biological signals
• ❌ Ambiguous protein group or isoform assignments
• ❌ Unstable quantification across DIA SWATH runs or TMT channels
• ❌ Poor normalization or QC masking true changes
• ❌ Overlooked PTM site inconsistencies
• ❌ Disconnected protein lists without pathway or functional context

🔍 What We Help You Analyze

🧬 Missing Value Imputation & Sensitivity Checks
Label-free or TMT data often have dropouts due to low abundance or instrument drift. We apply context-aware methods (MNAR left-censoring, MAR models) and confirm that differential expression is robust across imputation strategies.

🧪 Batch Effect Correction & Normalization
Large proteomics studies run across multiple batches, conditions, or instruments. We use PCA, replicate clustering, and empirical Bayes correction to ensure real signals aren’t buried by technical noise.

🔬 Protein Group & Isoform Inference
Shared peptides can distort group assignments. We validate unique vs. shared peptide calls, report clear protein groups and isoform limits, and provide a robust protein quantification pipeline curated beyond black-box tools.

📊 📊 Advanced Pipelines: DIA/SWATH, TMT, Label-Free
We combine best-practice open-source tools with custom scripts for library design, retention time correction, DIA SWATH quantification, peak shape validation, FDR control, and reproducible quantification across samples.

🧭 PTM Site & Phosphoproteomics Analysis
We resolve phosphosite ambiguities and confirm site-level quantification consistency to support robust PTM studies.

🧩 Functional Annotation & Pathway Context
Beyond tables of protein IDs, we map quantification results to pathways and biological processes so you can tell a clear biological story.

💡 Why Clients Choose Us

• - Exclusive focus on mass spectrometry data analysis - no wet-lab distractions
• - DIA/SWATH, TMT, label-free, PTM & phosphoproteomics expertise
• - Every dataset checked by senior experts - no black-box defaults
• - Custom pipelines designed for your study, not someone else’s template
• - Judgement-driven solutions for missing value imputation, batch correction, and protein group inference
• - Publication support: reviewer responses, method clarifications, clear output files
• - 150+ years of combined bioinformatics experience to handle any challenge

📚 Read Our Practical Proteomics Blog:
For a deeper look at the practical challenges we tackle every day - and how our pipelines solve them - check out our in-depth article: Practical Proteomics Data Analysis: Real Challenges and How We Solve Them

Explore the 10 Reasons Why Clients Choose Us →

Reason #1: 150 years of combined experience in bioinformatics
Reason #2: Deep understanding of both the biology and the computer
Reason #3: Top-level expertise possessed by our bioinformaticians
Reason #4: Wide range of bioinformatics and data modeling solutions that we cover
Reason #5: Researchers from 80 organizations can't all be wrong!
Reason #6: We are cost-effective
Reason #7: We guarantee to do it "right"!
Reason #8: We will assist you in paper reviews
Reason #9: We will assist you in grant writing
Reason #10: See how researchers have evaluated us

❓ Frequently Asked Questions

• ✔️ How long does analysis take? - Typically 2–4 weeks depending on data complexity.
• ✔️ How much data do you need? - We handle raw vendor files or pre-processed tables.
• ✔️ Can you help respond to reviewers? - Yes, we support clarifications and method write-ups.

Ready to get expert help with your proteomics project? Send us an inquiry, chat with us online (Mon–Fri, 9–5 U.S. Central Time), or connect with us any way you prefer!