Some Other Ions to Know About and Avoid

6 Some Other Ions to Know About and Avoid 

When analyzing peptides by LC-MS, especially with nano-LC, several of the contaminants listed earlier (Section 3.2.6) are encountered, particularly those that are PEG-based and various siliconates. There are also contaminants specific to peptide analysis, such as the products of autolysis, that occur when too much trypsin is added (or when the sample contains less protein than expected) (Table 3.9a). As a rule of thumb, trypsin should be present at a concentration that is 1% of the protein to be digested. Another common contaminant is keratin that is introduced by incorrect handling of samples or by accidental contamination during sample collection (Table 3.9b). 

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