📋 Workflow
Full workflow, products add-to-cart directly1
Protein extraction and quantification
2 hLyse cells/tissue to extract total protein, quantify and normalize
💡 Tip Deplete abundant interfering proteins if needed
⚠️ Caution Prevent degradation and oxidative modifications
🧪 Materials for this step (click to shop by spec/brand)
2
Digestion to peptides
4–16 hReduce/alkylate then digest protein to peptides with trypsin
💡 Tip Complete digestion improves coverage
⚠️ Caution Thorough reduction/alkylation avoids disulfides
🧪 Materials for this step (click to shop by spec/brand)
3
Labeling or tandem MS
2–4 daysOptionally TMT-label, separate/identify by LC-MS; or label-free DDA/DIA quantification
💡 Tip TMT multiplexes sample quantification
⚠️ Caution Stable LC-MS for reproducibility
🧪 Materials for this step (click to shop by spec/brand)
4
Database search and differential analysis
1–2 daysIdentify proteins by search software, identify differential proteins and pathway enrichment
💡 Tip Set FDR to control false positives
⚠️ Caution Rigorous stats to avoid over-interpretation
🧪 Materials for this step (click to shop by spec/brand)
⚠️ 5 Common Beginner Mistakes
- ① Incomplete digestion lowers coverage
- ② Abundant proteins mask low-abundance
- ③ Sampling/handling variation across batches
- ④ Uncontrolled FDR gives false positives
- ⑤ Improper missing-value handling biases
❓ FAQ
+Labeled vs label-free quantification?
Labeled (TMT) multiplexes with precision; label-free is higher-throughput, cheaper, slightly more variable.
+How to improve depth?
Deep fractionation, high-resolution MS, enrichment of low abundance or longer gradients.
+How to validate differential proteins?
Independently validate candidates by WB, ELISA or targeted MS (SRM/PRM).