How do I modify the parameter translation file for mass tolerance and threshold for reporting iTRAQ ratios

Answer 

Open ParameterTranslation.xml file using a plain text editor (notepad is safest) – DO NOT EDIT THIS FILE IN WORD OR ANY OTHER RICH TEXT EDITOR.

Mass Tolerance

1. Use Edit > Find From the Menu and Enter ‘MSTOLERANCE VALUE’

This should find the Key.

<MSTOLERANCE VALUE=”X.X” TYPE=”dalton”/>

Locate the Key within  the Correct Instrument Node for your Acquisition machine.

2. The Value (X.X) is the m/z tolerance for matching precursor ion m/z (observed and theoretical) for searches without MS recalibration as well as the initial fast search upon which MS recalibration is based.
3. The MSMSTOLERANCE VALUE key is identical but applied to MSMS scan types.

Standard Deviation

The standard deviation of delta m/z errors on the precursors that you expect for properly calibrated data for this instrument type. After recalibration, the m/z tolerance for matching precursor ion m/z (observed and theoretical) is given by multiplying mstolratio and MS_STANDARD_DEVIATION VALUE.  This element is not used if recalibration is off (ms=”false”) for the precursor data. You can use the PSPEP false discovery rate analysis to optimize the value for MS_STANDARD_DEVIATION VALUE fo the quality of the data acquired in your lab.  The process above can be used to find and alter the keys for the correct instrument type.

Reporting Threshold

The signal-to-noise (S/N) threshold for reporting an iTRAQ® reagent ratio. For any ratio, if the sum of the S/N of the numerator and the S/N of the denominator falls below this threshold, the ratio is not reported (the corresponding cell in the Peptide Quantitation table is blank). The S/N is peak area divided by peak area error.  This S/N value is controlled by the Value of the quant_threshold_sn=”x” key (for your instrument type)