The positive role and application of highly accurate mass measurements in 
proteomics is well documented. The new generation of hybrid FTMS and Q-TOF 
instruments, including the LTQ-Orbitrap (OT), is remarkable in their ability to 
routinely produce single-digit to subppm statistical mass accuracy while 
maintaining high analytical sensitivity. The use of mass calibrants (lock 
masses) to reduce the systematic error of mass-to-charge measurements has also 
been reported and, in some cases, incorporated in the instrument control 
software by the instrument manufacturers. We evaluated the use of one such 
calibrant in the OT (e.g., polydimethylcyclosiloxane, PCM) to study its impact 
on the rate of phosphopeptide annotation and found it to lack robustness under 
normal laboratory conditions. Therefore, we devised a strategy to improve its 
performance by increasing the external abundance of calibrant molecules in 
laboratory air. This resulted in a more robust performance of the preprogrammed 
lock mass recalibration feature as evidenced by improvements in both statistical 
mass accuracy and peptide annotation rates.