WBPaper00028360:Phospho-Sulfo-Modified_proteins

The protein identification was performed by PMF analysis with the spectra in the positive ion mode. Database searches against all entries of Refseq Release 13 were carried out using Biotools 2.2 (Bruker Daltonics) and MASCOT search engine (Matrix Science, London, UK). The search parameters allowed carbamidomethylation of Cys, partial oxidation of Met, 150 ppm for mass tolerance, and one missed cleavage per peptide. The protein identification results were accepted in consideration of the MASCOT score. Furthermore, the reliability of the results was confirmed by the additional information of the spectrum observed in the negative ion mode. Phosphorylation and sulfonation peptides were detected by Mass Spectrometry using the positive and negative ion modes with mono-ammonium phosphate as the matrix additive.

WBPaper00053615:SMO-1_target

Proteins were considered as SUMOylated if they were identified in at least 3 independent experiments, each protein identified with at least two peptides, FDR below 1% and not present in any of the control purifications from wild-type N2 worms or present with raw intensity greater than 10 times than in control purifications. Proteins that were modified by SUMO (smo-1). Using the strain RU86[smo-1(ok359); Is(psmo-1::smo-1gfp::3'UTRsmo-1] expressing HIS-GFP tagged SUMO, authors set up the purification of proteins modified by SUMO using immobilized metal ion affinity chromatography (IMAC).