Acetylation of lysines on affinity-purification matrices to reduce co-digestion of bead-bound ligands
David M. Hollenstein, Thomas Gossenreiter, Natascha Hartl, Dorothea Anrather, Markus Hartl, Margarita Maurer-Granofszky
on-bead digestion
affinity-purification
proteomics
BioID
streptavidin
acetylation
TurboID
interaction proteomics
LC-MS
Disclaimer
Abstract
In mass-spectrometry-based interaction proteomics on-bead digestion protocols are commonly applied after affinity-enrichment due to their simplicity and high efficiency. However, on-bead digestion often leads to strong background signals due to co-digestion of the bead-bound ligands such as streptavidin or antibodies. We present an effective, rapid and low-cost method to specifically reduce the peptide signals from co-digested matrix ligands. A short pre-incubation of matrix beads with Sulfo-NHS-Acetate (S-NHS-Ac) leads to acetylation of free amines on lysine side-chains of the bead-bound ligands making them resistant to Lys-C-mediated proteolysis. After binding of bait proteins to the acetylated beads we employ a two-step digestion protocol with the sequential use of Lys-C protease for on-bead digestion followed by in-solution digestion with trypsin. The strong reduction of interfering ligand peptides improves signal strength and data quality for the peptides of interest in liquid chromatography mass spectrometry (LC-MS).
Before start
This protocol consists of two parts: 1. bead acetylation, 2. on-bead digestion after the affinity enrichment experiment. The protocol for the enrichment depends on the experiment and is not part of this protocol. Please note that the preparations below only relate to part 1 (bead acetylation). Preparations necessary for on-bead digestion are mentioned in the according protocol step and in Materials.
Preparations for bead acetylation:
We recommend to prepare one large batch of beads for the same experimental series. The protocol allows the acetylation of 20 µL beads and can be simply scaled to the amounts required. Please determine and prepare the required reagents accordingly before starting the protocol.
When using magnetic beads all washing steps are performed using a magnetic rack to allow easy removal of buffer.
Using storage buffer is not necessary when the beads are used for affinity purification directly after washing. For longer storage it is highly recommended to prevent bacterial growth.
Steps
Acetylation protocol
Wash beads 3x with 100µl Reaction buffer , using the magnetic rack.
Remove supernatant after the final wash.
Add 19 µl Reaction buffer and 1 µl Sulfo-NHS-Acetate (100 mM) to obtain a final concentration of 5 mM Sulfo-NHS-Acetate.
Incubate 1h at room temperature with gentle mixing.
Discard supernatant and wash 3x with 100 µl Quenching buffer .
Use directly or store in 100 µL Storage buffer at 4°C for later use.
Affinity enrichment protocol
This step is not part of the protocol and will depend on the experiment, as for example BioID, enrichment via GFP and GFP-nanobodies, etc.
On-bead digest protocol
Prepare all reagents and materials as specified in Materials.
Remove remaining wash buffer from beads. Add 150 µL ABC buffer, gently mix and transfer the beads to a 0.2 mL PCR tube and discard supernatant.
Add 50 µL of 1 M urea in ABC buffer .
Add 2 µL DTT stock solution to reach a final concentration of 10 mM. Incubate for 30 min at room temperature.
Add 2 µL IAA stock solution to reach a final concentration of 20 mM. Incubate for 30 min at room temperature in the dark.
Quench remaining reactive IAA by adding 1 µL DTT stock solution (half the amount used in step 9) and incubate for 10 min at room temperature in the dark.
Add 1.5 µL (150 ng) Lys-C solution and digest over night at 25°C in the dark.
Transfer supernatant to a new PCR tube. Add 1.5 µL (150 ng) Trypsin solution and digest at 37°C for 5h.
Acidify sample by adding 3 µL 10% TFA to reach a final concentration of approximately 0.5%.
Proceed to desalting using according protocols (e.g. C18 StageTips or similar).
