Recommended parameters for QuiXoT strategies

These are recommended values for the weight calibration constant K, the minimum Vs acceptable and the filter to consider when performing statistics for the different strategies of QuiXoT.

Although they are a good starting point to analyse different experiments, users must be aware of the fact that these figures may vary strongly depending on the particular instrument used, how it is calibrated, and other general conditions that may affect the experiment. For this reason we urge QuiXoT users to calculate themselves the variables to use, in order to meet their particular needs, as well as the conditions of their experiments.

strategy	weight calibration constant (K)	minimum Vs	filter
18O LR	0.17	3.1	Vs>3.1 and st_Cterm=0 and q_Alpha<1.4 and q_Sigma<0.14 and q_A <> ' NaN ' and q_SD_A <> ' NaN ' and q_f<1.1 and q_f>0.5 and Label4 not like '%s_%' and Label4 not like '%p_%'
18O HR	40	-	st_Cterm = 0 and q_f >0.6 and q_f <1.1 and (q_A >0 or q_B>0) and label4 not like'%s_%' and label4 not like '%p_%'
SILAC LR	0.1 - 0.2	10	label5 not like '%no labeling%' and q_sigma>0.03 and q_sigma<0.25 and not (charge=1 and q_deltar>7) and not (charge=2 and q_deltar>13) and q_deltamz<0.1 and q_deltamz>-0.1 and Vs>10 and numlabel1>0
SILAC HR	10 - 20	100	q_A > 0 and q_B > 0 and not (charge = 1 and q_deltaR > 6) and not (charge =2 and q_deltaR > 12) and not (charge =3 and q_deltaR > 18) and label4 not like '%s_%' and label4 not like '%p_%' and Vs>100
iTRAQ TOFTOF	200 - 300	155	q_fittedMass_114 <> ' 0 ' and q_fittedMass_115 <> ' 0 ' and vs>155 and label4 not like '%s_%' and label4 not like '%p_%'
iTRAQ PQD	14 - 17	200	q_fittedMass_114 <> ' 0 ' and q_fittedMass_115 <> ' 0 ' and Vs>200 and label4 not like '%s_%' and label4 not like '%p_%'

Notes

We are assuming that label4 is used to label scans or peptides which should be removed for some reason. It is a good habit to label them with a code like s_outlier or s_badfit at scan level, or like p_methionine or p_partialdig at peptide level. We can take advantage of this notation to filter these bad scans or peptides in the way shown above.