compared with
Current by Louis Felix Nothias
on Apr 03, 2017 09:36.

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h2. Running the Dereplicator on GNPS

{color:#000000}{*}BASIC OPTIONS:*{color}

*  \-\- Precursor Ion Mass Tolerance: * {color:#000000}This value specifies how much fragment ions can be shifted from their expected{color} {color:#000000}m{color}{color:#000000}/{color}{color:#000000}z{color} {color:#000000}values. Default value is ± 0.02 Da for high-resolution instruments (q-TOF, q-Orbitrap) and ± 2.0 0.5 Da for low-resolution instruments (ion traps, QqQ).{color}

*  \-\- Fragment ion Mass Tolerance:* {color:#000000}This value specifies how much fragment ions can be shifted from their expected{color} {color:#000000}m{color}{color:#000000}/{color}{color:#000000}z{color} {color:#000000}values. Default value is ± 0.02 Da for high-resolution instruments (q-TOF, q-Orbitrap) and ± 2.0 0.5 Da for low-resolution instruments (ion traps, QqQ).{color}

{color:#000000}*  \-\- Search analog (VarQuest)*{color}{color:#000000}: The VarQuest algorithm can search for analogs of known natural products in MS/MS data using Dereplicator. VarQuest is a modification-tolerant database search tool that discovers unexpected modifications in a blind mode. Since the computational space for variable PNP identification is computationally expensive, VarQuest first constructs a set of feasible PSM using a simple scoring approach and further filters out this set using a rigorous scoring method. Using VarQuest will increase the job time.{color}