ProtiFi Si-Trap 96-well Mini Kit for Multi-Omics Sample Preparation

ProtiFi Si-Trap™ 96-well Mini Kit is a 96-well multi-omics sample-preparation system designed to separate and capture multiple classes of biomolecules from a single biological sample for downstream protein, metabolite, and lipid analysis. The kit processes samples corresponding to 25–200 µg of total protein per well and combines small-molecule fractionation with subsequent processing of captured proteins directly within the Si-Trap™ plate. 

Unlike S-Trap™ processing, Si-Trap™ begins with detergent-free sample dissolution. Following neutralization and organic-solvent denaturation, proteins are captured within the derivatized porous matrix while metabolites and lipids are recovered from the flow-through. Captured proteins are subsequently reduced, alkylated, washed, and enzymatically digested directly within the plate.

Si-Trap™ Technology

Si-Trap™ is designed to prepare multiple omics fractions from one sample. The starting material is first dissolved without detergent. Following addition of Binding Solution, proteins are captured through multiple weak-affinity interactions within the derivatized pores of the Si-Trap™ matrix.

Small molecules remain in the flow-through:

• metabolites are subsequently eluted using an MS-compatible solution,
• lipids can optionally be separated following addition of Solution L and liquid-phase separation,
• proteins remain trapped within the plate for downstream proteomic processing.

Captured proteins are reduced and alkylated in situ, washed, and digested with the protease of choice. The resulting peptides are then eluted for LC-MS/MS analysis. 

Important: unlike the S-Trap™ workflow, the current Si-Trap™ 96-well Mini Kit protocol requires that the starting sample does not contain detergent. 

Standard Multi-Omics Workflow

1. Sample dissolution/lysis using Si-Trap™ Lysis Solution A
2. Optional sonication for DNA-containing samples
3. Addition of Binding Solution A
4. Optional addition of Solution L for lipid analysis
5. Transfer to the Si-Trap™ 96-well Mini Plate
6. Protein trapping
7. Collection of the small-molecule flow-through
8. Metabolite elution
9. Optional separation and collection of the lipid fraction
10. Concentration of metabolite and optional lipid fractions
11. Protein reduction and alkylation in the plate
12. Protein washing
13. Protease addition
14. Digestion at 47 °C
15. Peptide elution
16. Preparation of individual fractions for downstream MS analysis. 

Technical Specifications

• Format: 96-well plate with reagents and accessories
• Application: Multi-omics sample preparation
• Biomolecule Classes: proteins/peptides, metabolites, optional lipids
• Sample Range: 25–200 µg total protein
• Approximate Well Capacity: 450 µL
• Standard Centrifugation: 2,000 × g for 2 min
• Alternative Flow Methods: vacuum or positive pressure
• Plate Pre-Equilibration: not required
• Reduction/Alkylation: 80 °C for 30 min
• Protein Washing: 250 µL Wash Solution, 3 times
• Protease Solution Volume: 125 µL
• Recommended Trypsin-to-Protein Ratio: 1:10 (w/w)
• Digestion: 1–2 h at 47 °C
• Peptide Elution 1: 80 µL Digestion Solution
• Peptide Elution 2: 80 µL Elution Solution
• Optional Hydrophobic Peptide Elution: 80 µL 50% ACN / 0.2% formic acid
• Downstream Analysis: LC-MS / LC-MS/MS

Kit Contents

PN K006-96MNI-0001KT includes:

• 1 Si-Trap™ 96-well Mini Plate
• 1 × 2.0 mL 96-well Waste Plate
• 2 × 1.0 mL 96-well Collection Plates
• 2 Silicone Mats
• Solution 1 – Lysis Solution A: 2 × 2.5 mL
• Solution 2 – Binding Solution A: 1 × 5.0 mL
• Solution 3 – Metabolite Elution Solution: 1 × 26.0 mL
• Solution 4 – Reductant/Alkylator:
  • Solution 4B: 1 × 5.0 mL
  • Solution 4A: 1 × 300 µL
  • Solution 4R: 1 × 500 µL
• Solution 5 – Wash Solution: 3 × 26.0 mL
• Solution 6 – Digestion Solution: 1 × 30.0 mL
• Solution 7 – Elution Solution: 1 × 8.0 mL. 

Not Included

Additional materials required for the workflow include:

• protease of choice, such as trypsin,
• LC-MS-grade water,
• LC-MS-grade acetonitrile,
• LC-MS-grade formic acid.

For lipid fractionation, Si-Trap™ Solution L – Lipid Elution Solution is required and is sold separately. 

Storage

• Si-Trap™ 96-well Mini Plate: up to 1 year at 4 °C
• Solution 1: up to 1 year at room temperature when tightly closed; do not heat
• Other supplied solutions: up to 1 year at −20 °C

After thawing at 4 °C, solutions should be mixed thoroughly to redissolve any precipitate. 

Typical Applications

• Multi-omics
• Integrated proteomics and metabolomics
• Proteomics, metabolomics, and lipidomics from a single sample
• High-throughput multiomics
• Bottom-up proteomics
• LC-MS/MS peptide preparation
• LC-MS metabolite analysis
• Lipidomics LC-MS
• Cell and tissue samples
• Complex biological samples
• Cohort studies
• Automated 96-well sample preparation