Recommended parameters for QuiXoT strategies - Revision history

Mtrevisan at 12:54, 27 April 2017

2017-04-27T12:54:45Z

Mtrevisan at 12:54, 27 April 2017

2017-04-27T12:54:24Z

Mtrevisan at 12:54, 27 April 2017

2017-04-27T12:54:01Z

Mtrevisan: cat

2013-09-13T15:48:21Z

cat

Mtrevisan at 14:22, 13 September 2013

2013-09-13T14:22:31Z

Mtrevisan: creation

2013-09-13T13:45:54Z

creation

New page

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

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.

{|class="wikitable"
|-
!strategy||weight 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.

[[Category:QuiXoT]]

← Older revision		Revision as of 12:54, 27 April 2017
Line 1:		Line 1:
−	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]].	+	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.		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.

← Older revision		Revision as of 12:54, 27 April 2017
Line 1:		Line 1:
−	These are ''recommended'' values for the weight constant ''K'', the minimum ''Vs'' acceptable and the filter to consider when performing statistics for the different strategies of [[QuiXoT]].	+	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.		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.

← Older revision		Revision as of 15:48, 13 September 2013
Line 25:		Line 25:

	[[Category:QuiXoT]]		[[Category:QuiXoT]]
		+	[[Category:Useful information]]

← Older revision		Revision as of 14:22, 13 September 2013
Line 1:		Line 1:
−	These are ''recommended'' values for the weight constant ''K'', the minimum ''Vs'' acceptable and the filter to consider when performing statistics for different strategies.	+	These are ''recommended'' values for the weight 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.		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.

@@ Line 5: / Line 5: @@
 {|class="wikitable"
 |-
-!strategy||weight constant (K)||minimum Vs||filter
+!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_%'