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0
NextStep
0
Undefined
Consensus
Example Consensus Workflow with MS Ana
Standard consensus workflow applicable to any search engine. No specific changes in the consensus workflow are required to work with MS Ana.
http://thermo.magellan.com/owl/DataTypes/WithDecoys
http://thermo.magellan.com/owl/DataTypes/WithDecoys
Identified or Quantified
All
Globally by Search Engine Type
10
0.05
0
0 ppm
0
0
0
0
0
0
0
0
0
0
Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score
Best match
standard
75
http://thermo.magellan.com/owl/DataTypes/WithDecoys
http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP
http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue
http://thermo.magellan.com/owl/DataTypes/Validated
http://thermo.magellan.com/owl/DataTypes/WithDecoys
http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP
http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue
http://thermo.magellan.com/owl/DataTypes/Validated
http://thermo.magellan.com/owl/DataTypes/WithDecoys
Automatic (Control peptide level error rate if possible)
0.01
0.05
0.01
0.05
q-Value
False
False
http://thermo.magellan.com/owl/DataTypes/Validated
http://thermo.magellan.com/owl/DataTypes/Validated
http://thermo.magellan.com/owl/DataTypes/Filtered
http://thermo.magellan.com/owl/DataTypes/Filtered
http://thermo.magellan.com/owl/DataTypes/Filtered
High
False
6
False
1
False
False
http://thermo.magellan.com/owl/DataTypes/Filtered
http://thermo.magellan.com/owl/DataTypes/Filtered
http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore
http://thermo.magellan.com/owl/DataTypes/Filtered
http://thermo.magellan.com/owl/DataTypes/Validated
http://thermo.magellan.com/owl/DataTypes/Filtered
http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore
True
http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore
http://thermo.magellan.com/owl/DataTypes/Validated
0.01
0.05
http://thermo.magellan.com/owl/DataTypes/Filtered
http://thermo.magellan.com/owl/DataTypes/Filtered
False
False
1
InitialStep
0
Undefined
Processing
Example Processing Workflow with MS Ana
Click the MS Ana Node and under "1. Input Data" select a registered Spectral Library and Protein Database (optional) to get started. Tweak parameters to fit your experiment.
Use MS1 Precursor
True
True
True
0
0
0
0
0
0
350 Da
5000 Da
0
1
(Not specified)
Is Not MS1
(Not specified)
0
1000
Is Full
(Not specified)
1.5
Automatic
ITMS
MS2
CID
+
60000
30000
2.5 Da
5.5 Da
http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore
http://thermo.magellan.com/owl/DataTypes/WithDecoys
http://thermo.magellan.com/owl/DataTypes/WithDecoys
Ion Shift
False
False
True
10 ppm
20 ppm
5
15
15
True
15
False
500
300
<Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" />
False
False
False
False
False
True
False
False
True
False
300
True
False
http://thermo.magellan.com/owl/DataTypes/WithDecoys
http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP
http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue
http://thermo.magellan.com/owl/DataTypes/Validated
0.05
0
True
0.01
0.05
q-Value
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