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.
What is the standard solvent for the Pierce Quantitative Peptide Assays & Standards (Cat. No. 23275)?
The solvent for the Pierce Quantitative Peptide Assays & Standards (Cat. No. 23275) is 50mM ammonium bicarbonate.
Find additional tips, troubleshooting help, and resources within our Protein Assays and Quantitation Support Center.
When I quantitate my mass spec peptide sample with the Pierce Quantitative Colorimetric Peptide Assay, I get different results than when I use the Pierce Quantitative Fluorometric Peptide Assay. Which is best to use for the most accurate quantitation?
Since the different peptide assays use different chemistries to measure peptides, they may result in different results. Interfering compounds are the most common source of background and inaccurate measurements. Please note that the fluorometric peptide assay is not recommended for peptides which have been modified using TMT reagents.
Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.