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If you use a peptide desalting method that doesn't retain anionic or neutral compounds and those polymers fall into that category you need not worry about them WRT MS contamination. I use CDS Empore SCX or SDB-RPS (difference is the degree of sulfonation, SCX has more sulfonic acid groups) for all desalting. For a 100ul digest volume: Dilute digest 1:10 into 90% Acetonitrile, 1% TFA Apply to an appropriately sized* Empore SDB-RPS tip and spin until dry. Wash with 0.5ml of 90% Acetonitrile, 1% TFA, spin until dry. Wash with 0.5ml of 10% Acetonitrile, 0.1% TFA, spin until dry. Elute with 150ul of 80% Acetonitrile, 5% NH4OH directly into injection vials. Dry down, then dissolve in appropriate volume of 0.1% formic acid. Inject directly onto separation capillary column. *I use 1-4 2mm diameter plugs of the SCX or SDB-RPS material packed into a P1000 pipet tip. The two considerations for this method are that you can digest the sample in any matrix that doesn't inhibit the enzymatic activity of Trypsin, and any matrix components that are anionic or neutral are removed at the above desalting stage. This means your polymers if not cationic will be of no consequence downstream. Nor will any neutral or anionic detergent. I've done digests in RIPA buffer. I've started using Triton X114 for isolating membrane proteins for proteomics analysis and have observed no detergent contamination following the above desalting workflow. The S-Trap method is good if your protein prep is in a matrix that is inhibitory to Trypsin digestion, but otherwise not necessary. Manipulations at the protein level are more prone to variable losses than are manipulations downstream at the peptide level. Therefore, do as little as possible at the protein stage and shift sample prep manipulations to the stage after digestion to reduce losses and decrease variability when possible. Best regards, Brian