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.