Problem | Potential cause | Solution |
---|---|---|
Poor quality LC-MS run | Problem with Sample or with HPLC column | Run a peptide standard; if standard = poor, replace HPLC if standard = fine, problem with sample |
Poor electrospray stability or overall low signal intensity | Insufficient desalting | More washes of sample during peptide recovery |
Sudden increase in HPLC pressure | Particulate debris in the sample | Replace HPLC column, lines, junctions to autosampler, and/or the rotor and stator of the autosampler valve; Centrifuge peptide sample at 16000 x g, transfer top 90% of volume |
Poor chromatography – fronting peaks (peak skews to earlier retention time) | Column capacity overloaded due to overly concentrated peptide sample | Dilute sample |
Poor chromatography – tailing peaks (peak skews to later retention time) | Residual reactive silanol groups in the stationary phase, or improper formulation of the mobile phases (pH) | Replace HPLC column and/or HPLC buffers |