Frequently asked questions
Which species can be used with Phosphomatics
The databsaes of substrate-kinase relationships used in Phosphomatics cover Human, Mouse and Rat phosphoproteomes. Data for other species can still be uploaded and statistical analysis can be performed however no upstream kinase data will be available.
Note that KSEA analysis is currently limited to Human phosphoproteomes.
How does phosphomatics handle multiplicity?
Some search engines provide abundances of phosphorylation sites observed in different multiplicity states. If multiple sets of quantitation values are detected by Phosphomatics for the same phosphorylation site, these are assumed to denote sites in different multiplicity states and the quantitative values are summed to give a single value for the site.
Should the uploaded data be log2 transformed?
Ideally, no. Phosphomatics assumes that raw abundances are provided in the input data. While uploading log-transformed data does not necessarily cause problems, summation of quantitative values for site abundances for phosphosites detected in diffeent multiplicity states will create erroneously high abundances if the uploaded data is already log transformed.
How long does the initial data processing take?
Initial data processing should not take longer than a few minutes. If 15 or more minutes has elapsed, a problem has likely occured. Please contact us and let us know.!
I'm getting errors during the initial data processing!
There are a number of reasons why this might happen. Some common things to check are:
- Make sure that the names you supply for treatment groups and sample aliases are compatible with R variable types. For example, remove spaces, special characters and ensure that names do not begin with a digit.
- Make sure that some phosphorylation sites remain after data filtering. For example, if you submit 9 samples, but set filters that require 10 or more valid values, no sites will remain and the analysis will fail.
- Phosphomatics can handle cases where a phosphorylation site is assigned to a protein group by unwrapping the group and considering each protein separately. In these cases, the protein UniProt identifiers are split on a ';' character. Since the residue number of the identified site may differ based on the protein, phosphomatics will also split the position column at a ';' character to retrieve the position for each protein respectively. It is essential in these cases that the number of proteins in the UniProt Identifier column match the number of integer phosphorylation positions. Since many software will provide separate columns for all proteins in a group and 'leading' or 'majority' proteins, check that the correct columns have been selected.