Data-Independent Acquisition (DIA)
Our DIA mass spec service offers higher protein coverage than Data Dependent Acquisition (DDA) methods. In contrast to DDA, which fragments only peptide precursors meeting certain cutoffs, the DIA approach fragments all peptides across a predefined peptide precursor window during the entire nanoLC gradient.
Main advantages of DIA proteomics:
- Ideal for comparing protein levels across sample groups
- Increased protein coverage on low abundance proteins
- Can be applied to any LC-MS/MS project involving any protein samples
We have optimized every step of DIA workflows from sample preparation to nanoLC-MS/MS and data analysis.
Example 1: DIA analysis of media sample
In our internal study comparing DIA and DDA for the same media sample, DIA outperformed DDA across every peptide threshold. The greatest gains were seen at the lower-abundance confidence levels:
- >5 peptides: 222 proteins detected with DIA vs. 144 with DDA
- >2 peptides: 407 proteins detected with DIA vs. 211 with DDA
| Type of Acquisition | Proteins Detected | ||||
|---|---|---|---|---|---|
| >30 peptides | >20 peptides | >10 peptides | >5 peptides | >2 peptides | |
| DDA | 6 | 27 | 68 | 132 | 197 |
| DIA | 8 | 34 | 112 | 222 | 407 |
Overall, the experiment identified 478 proteins with DIA compared with 289 proteins with DDA, demonstrating substantially improved proteome coverage.
DIA experimental procedure
- Sample preparation: Sample clean up, protein extraction, measure/adjust protein concentration, and trypsin digestion
- nanoLCMSMS: Peptides separated and analyzed by ThermoFisher Ultimate 3000 & Orbitrap Exploris
- Data analysis: Protein identification and quantitation by DIANN
- Data output: Results are generated using Applied Biomics’ proprietary scripts
Sample Info
Sample type: We accept in-solution, in-gel samples or IP beads for this service.
Protein amount: 5-200 µg of total protein from each sample.
Protein concentration: 5-20 mg/ml is preferred for in-solution samples..
Buffer: Please feel free to submit samples in whichever buffer that you would normally use. Please inform our scientists about buffer composition. Additional charge will apply on samples: 1) <4 mg/ml in concentration; 2) requiring extensive prep such as protein eluting, buffer exchange or serum abundant protein depletion.
Biohazardous Materials: We do NOT accept samples containing any biohazardous materials. If your samples contain any biohazardous materials, please make sure to deactivate them completely using the appropriate procedure and declare them in the order form. In addition, we do NOT accept any samples containing Level 4 biohazardous materials even if they are deactivated. Please view here for the rank of biohazardous materials.
Sample type: Please inform our scientists about your sample type. We will send you additional tips for each sample type.
Pricing
| Services Description | Academic/Governmental Labs | Industrial/Commercial Labs | ||
|---|---|---|---|---|
| Code | Price | Code | Price | |
| DIA Experiment | 335A | call for price | 335N | call for price |
Turnaround time is 7-9 days. Price covers the following:
- Reduction, alkylation and Trypsin digestion
- NanoLC-MS/MS with DIA settings
- DIA data analysis against one species in NCBI or SwissProt database
- Data report
Price does NOT cover sample preparation