Many users contact us asking what the Quantitative value tags are. These can be found in the in-program help. Open Scaffold Q+S 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 quantitative 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: This tag 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+S Quantitation Module
The Q+S Quantitation Module defines quantitative values as missing when isobaric tags, isotopic labels or precursor intensity values have either a raw value of zero or 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.