Week 5 (6-5-06)

Well I had a nice blog but I guess it didn't save!

I didn't have many questions and those that I did have were noted in the comment on ProteomeCommons.

I am through with June and moving on to August

August

I worked on:
-Genetic Association, Post-translational Modification, and Protein-Protein Interactions in Type 2 Diabetes Mellitus
-Quantification of Gel-separated Proteins and Their Phosphorylation Sites by LC-MS Using
-An Immunoproteomic Approach for Identification of Clinical Biomarkers for Monitoring Disease Application to Cystic Fibrosis
-Metabolic Activation-related CD147-CD98 Complex
......but Blogger was down- All of these had data but didn't publish.

Proteome Analysis of the Rice Etioplast: Metabolic and Regulatory Networks and Novel Protein Functions
-Has data but did not publish
- Is carboxyamidomethylated the same as Carbamidomethylation?

Difference in Mass Analysis Using Labeled Lysines (DIMAL-K)
- Has data but did not publish
- What are "Acetimidoyl and propionimidoyl were set as fixed lysine modifications"
- Is there a name for this labeling--- "either LPS-treated samples were labeled with S-methyl thioacetimidate, and the untreated ones were labeled with S-methyl thiopropionimidate, or inversely LPStreated samples were labeled with S-methyl-thiopropionimidate, and the untreated ones were labeled with S-methyl-thioacetimidate." of "12C isotopic peaks"


Large Scale Protein Identification in Intracellular Aquaporin-2 Vesicles from Renal Inner Medullary Collecting Duct
-Has data but did not publish
- Is "carboxyamidomethylation" the same as Carbamidomethylation?

Systematic Analysis of the Epidermal Growth Factor Receptor by Mass Spectrometry Reveals Stimulation-dependent Multisite Phosphorylation
-Has data but did not publish
-Used "custom made desalting/concentration columns used in series"...what should I put?
- Just to make sure, if I see "S-carbamidomethylation", I should list it as a modification even if the paper was not refering to mods when carbamidomethylation was mentioned.

Differential Impact of Environmental Stresses on the Pea Mitochondrial Proteome
-Has data but did not publish

Multiple Reaction Monitoring to Identify Sites of Protein Phosphorylation with High Sensitivity

-Has data but did not publish

- Says “In general, transitions were included for all tryptic peptides (maximum one missed cleavage) containing Ser, Thr, or Tyr residues with either one or two modifications” …What are the modifications?

- what would “deamidation” or “phosphorylation” be a modification of?

Novel Src Homology 3 Domain-binding Motifs Identified from Proteomic Screen of a Pro-rich Region

-Has data but did not publish

- was not a mass spec paper