What do the Quantitative Value Tags Mean: Value Missing, No Values, Reference Missing, or No Data

Many users contact us asking what the Quantitative value tags are. These can be found in the in-program help. Open Scaffold Q+ and go to Help > Help Contents... and search for the term Quantitative value tags. Here they are:

Quantitative Value Tags

When selecting Display Options that includes the Log2 Fold Change of a quantity, three types of tags might appear in the samples table’s cells:

  • Value Missing: The “numerator” of the Fold change is marked as missing and the log of ratio goes to infinity. This case might happen when a protein group has not been detected in a particular Quant Sample.
  • No Values: Both the numerator and the reference are marked as missing values.
  • Reference Missing: The reference of the ratio is marked as a missing value.

Another tag might appear in the following circumstances is:

  • No Data: It appears for the “Log2 Fold Change” and “Fold Change Ratio” display options when the selected protein has no exclusive quantifiable peptides assigned to it.

Treatment of Missing Data by the Q+ Quantitation Module

The Q+ Quantitation Module defines Quantitative values as missing when isobaric tags or isotopic labels or precursor intensity values have either a raw value of zero or the values fall below the “Minimum Dynamic Range.”

Within each MS-Sample a “missing value” is assigned the larger value between (a) the minimum positive logged intensity acquired and (b) the value whose z-score is -4 for the distribution of all logged values in the MS-Sample.

It is possible to remove from the calculation spectra with missing values in the reference channel through the Spectrum Quality filter option available in the Quantitative Settings dialog.

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