response = query_engine.query("find me protocol for trypsin purification by affinity chromatography. include relevant citation.")  
print(response)

<think>
Okay, I need to figure out how to respond to this query about finding a protocol for trypsin purification using affinity chromatography and include the relevant citation. The user has provided some context from a PDF file, so I should use that information.

First, looking through the pages provided:

- Page 948 mentions the significance of affinity purification in reducing unmatched peptides and improving proteomic routines. It also lists keywords including affinity chromatography, arginine, benzamidine, etc.
  
- Page 951 discusses the use of Arginine Sepharose and Benzamidine Sepharose for trypsin purification. It explains that these sorbents bind trypsin through interactions in the catalytic pocket.

In section 2.3 under page 949, there's a detailed protocol:

- They used Arginine Sepharose 4B (ASE) and Benzamidine Sepharose 4 Fast Flow (BSE).
- The equilibration buffer was 50 mM ammonium bicarbonate.
- Sorbents were prepared by mixing the wet gel with an equal volume of buffer in a Falcon tube.
- Trypsin solutions (1 ml) were applied for binding.

So, compiling this into a protocol, I can outline the steps based on what's described. The relevant citation is from the same source, which is the journal article itself: Journal of Proteomics 74 (2011) 948–957.

I should present this concisely, ensuring all key steps are included and cite the source properly.
</think>

To purify trypsin using affinity chromatography:

1. **Prepare Sorbents**: Use Arginine Sepharose 4B (ASE) and Benzamidine Sepharose 4 Fast Flow (BSE).
2. **Equilibrate**: Equilibrate both sorbents in 50 mM ammonium bicarbonate buffer.
3. **Sorbent Suspension**: Mix the wet gel with an equal volume of equilibration buffer thoroughly.
4. **Binding Step**: Apply 1 ml trypsin solution to the affinity column for binding.

**Citation**: Journal of Proteomics 74 (2011) 948–957.

This protocol effectively purifies trypsin, enhancing its utility in proteomic studies by minimizing autolysis and improving peptide matching.