Should I desalt my peptide samples before enrichment using the High Select Phosphopeptide Enrichment Kits?
Yes, we do recommend desalting peptide samples before enrichment when using High-Select Fe-NTA and TiO2 phosphopeptide enrichment kits. This helps ensure optimal results by removing detergents and salts that can interfere with the enrichment process.
Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.
In the SMOAC protocol (https://www.thermofisher.com/blog/learning-at-the-bench/wp-content/uploads/sites/13/2024/10/High-SelectTM-SMOAC-Protocol.pdf), can I enrich with High-Select Fe-NTA kit first?
No. It is important to enrich with the TiO2 kit (Cat. No. A32993) first. Afterwards, the flow-through and wash fractions from this enrichment can be processed with the Fe-NTA kit (Cat. No. A32992). If this order is reversed (that is, Fe-NTA before TiO2), there will be 2 consequences as follows:
1. There will not be any significant additional recovery of peptides (maybe just a few more peptides).
2. There will be no enrichment for the multiple phosphorylated peptides, so those would be lost.
Find additional tips, troubleshooting help, and resources within our Protein Purification and Isolation Support Center.
Why do you offer two phosphopeptide enrichment kits: the High-Select TiO2 kit (Cat. No. A32993) and the High-Select Fe-NTA kit (Cat. No. A32993)?
The two phosphopeptides enrichment kits, Fe-NTA and TiO2, enrich a complementary set of phosphopeptides.
Our R&D has developed a Sequential enrichment of Metal Oxide Affinity Chromatography (see https://assets.thermofisher.com/TFS-Assets/CMD/posters/PO-65032-SMOAC-Phosphoproteomics-Peptides-ASMS2017-PO65032-EN.pdf and https://www.thermofisher.com/blog/learning-at-the-bench/wp-content/uploads/sites/13/2024/10/High-SelectTM-SMOAC-Protocol.pdf?CID=bid_mic_r04_jp_cp0000_pjt0000_bid00000_0so_blg_protein_analysis_mass_spectrometry_bid_ts_mbr_24065_Social_LAB) where flow-through and wash fractions from TiO2 enrichment were combined and subjected to Fe-NTA enrichment. This sequential enrichment provides impressive coverage of phosphoproteomes.
Find additional tips, troubleshooting help, and resources within our Protein Purification and Isolation Support Center.
What are the differences between the old Fe-NTA kit (Cat. No. 88300) and the new High-Select Fe-NTA kit (Cat. No. A32992)?
There are four differences between the Fe-NTA kit (Cat. No. 88300) and the new High-Select Fe-NTA kit (Cat. No. A32992) kit as follows:
1. The selectivity - the ratio of number of phosphopeptides over total peptides - was significantly improved to 99% with Cat. No. A32992, because the reagents were extensively optimized for the phosphopeptide selection.
2. The phosphopeptide yield was also increased to 33 µg based on quantitative colorimetric peptide assay (Cat. No. 23275).
3. The reagent is a pre-formulated format, so mixing reagent to prepare the working solution from stock solutions provided in the old kit (Cat. No. 88300) is not necessary, so it is easier to handle.
4. The enrichment protocol is optimized and streamlined, which means there are many fewer steps than with Cat. No. 88300. Thus, it takes <45 min to finish the entire protocol compared to 2 hours with the old kit (Cat. No. 88300).
Find additional tips, troubleshooting help, and resources within our Protein Purification and Isolation Support Center.
I have poor phosphopeptide enrichment specificity using either the High-Select TiO2 Phosphopeptide Enrichment Kit or the High-Select Fe-NTA Phosphopeptide Enrichment Kit. What should I do?
Here are some tips:
- Check the expiration date in order to assure that all components are still good.
- Keep TiO2 tips protected from light during storage.
- Make sure that you are using the correct buffer component for resuspension of your sample, and that the sample is very thoroughly dried and resuspended well.
- When incubating peptide samples with the Fe-NTA kit, ensure that you avoid end-over-end rotation or vortexing; instead gently tap the column to disperse the resin.
- When removing plugs from columns, be sure to avoid pushing liquid back into the column from the plug reservoir.
- After elution, do not store the phosphopeptides in the elution buffer but immediately proceed to drying the sample before storing at -80 degrees C until mass spec analysis.
Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.