The purified and quantified proteins were stored at 4 °C.
Out of the GO annotated quantified proteins, 45% and 48% were annotated with a nuclear localization from brain and liver, respectively, with a similar distribution of molecular nuclear functions (Figure 5).
We quantified proteins from up to ten samples using isobaric chemical tags (tandem mass tags, TMT) (McAlister et al., 2012) and MS3 mass spectrometry.
Cells were lysed, protein concentration of the lysates quantified, proteins separated by NuPAGE system (Invitrogen, Carlsbad, CA), and immunoblotted as described previously [ 7].
The raw data and summary list of identified and quantified proteins are available through the Computational Proteomics Analysis System upon request.
To determine whether the metabolic endotoxaemia also affected other insulin-responsive organs, we quantified proteins involved in liver and skeletal muscle metabolism.
The resulting peptides were fractionated using RP-HPLC analyzedyzed by CE MS yielding a total of 28 538 quantified peptides that correspond to 3 272 quantified proteins.
Together, this suggests that a large proportion of identified and quantified proteins in the purified, but not crude, samples show specific changes in abundance relating to SUMO modification status, as well as a dependence upon infection for SUMO conjugation state.
This example serves to illustrate the diverse types of analysis that may be performed to obtain protein expression values (i.e. quantified proteins in one or more samples) from raw MS data.
