Week 3 5/22/06

When downloading some of the articles, there was a supplemental data file next to the PDF link. I opened some of them up and fouund tables/xcel files that have some raw data(?) Is that what their data would look like or are those just summaryh tables?


A Comparative Proteomic Strategy for Subcellular Proteome Research: Icat Approach Coupled with Bioinformatics Prediction to Ascertain Rat Liver Mitochondrial Proteins and Indication of Mitochondrial Localization for Catalase
-Has data but did not publish

Comparative Proteome Analysis of Saccharomyces cerevisiae Grown in Chemostat Cultures Limited for Glucose or Ethanol
-Has data but did not publish

Proteome Analysis of the Human Mitotic Spindle
-Has data but did not publish
- did not give much info....refered to many papers about the digest, etc.

A Global Approach Combining Proteome Analysis and Phenotypic Screening with RNA Interference Yields Novel Apoptosis Regulators
-Has data but did not publish
- Uses Jurkat T cells or HeLa cells. What do I put for eVOC#?
- Variable Mod= "pyro-Glu formation at Nterminal Gln" and modification of cysteines by acrylamide" How is this written?
- Is "acetylation of the N terminus" written "N-term 42.010565"?

A Universal Strategy for Proteomic Studies of SUMO and Other Ubiquitin-like Modifiers
-Has data but did not publish
- Is "EKMax™ Enterokinase" a digestion?
- Is "pulselabeled with 200 Ci of trans-35S label" a label?

Identification of Sumoylated Proteins by Systematic Immunoprecipitation of the Budding Yeast Proteome
-Has data but did not publish
- I do not think that this used mass spec so I put n/a in almost all of the fields

Rapid Purification and Mass Spectrometric Characterization of Mitochondrial NADH Dehydrogenase (Complex I) from Rodent Brain and a Dopaminergic Neuronal Cell Line
-Has data but did not publish
- DID not list any Mods

FEB Articles

Characterization of Gel-separated Glycoproteins Using Two-step Proteolytic Digestion Combined with Sequential Microcolumns and Mass Spectrometry
-Has data but did not publish
- I have no idea what organism the proteins came from.....

Proteomics of the Injured Rat Sciatic Nerve Reveals Protein Expression Dynamics During Regeneration
-Has data but did not publish
- Does "For MS, the samples were loaded in a nanoelectrospray capillary (pulled from borosilicate capillary GC 100F-10 with a micro-capillary puller) or spotted onto a MALDI target." mean that it used MALDI and ESI?
- Does this mean that had a modification (the reference to Iodoacetamide) "equilibration in 6 M urea/2% SDS/2.5% iodoacetamide/50"

A Proteomic Analysis of Lysosomal Integral Membrane Proteins Reveals the Diverse Composition of the Organelle
-Has data but did not publish
- How do I write the Var. Mod "guanidinylation" and "N-acetylation of the N-terminal"

High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry
-Has data but did not publish
-Is "Proteins from 100
l of serum were used in isolation and isotope labeling of formerly N-linked glycopeptides" isotopically labeling?


Proteome Changes in Ovarian Epithelial Cells Derived from Women with BRCA1 Mutations and Family Histories of Cancer
-Has data but did not publish

A Systematic Characterization of Mitochondrial Proteome from Human T Leukemia Cells*
-Has data but did not publish

High Throughput Proteome Screening for Biomarker Detection
-Has data but did not publish
- Is " Peptides—Fmoc (N-(9-fluorenyl) methoxycarbonyl)-derivatized stable isotope monomers containing one 15N and five to nine 13C atoms were from Cambridge Isotope Laboratories (Andover, MA)" a label (Fmoc).
- How do I write "asparagine to aspartic acid at the site of carbohydrate attachment" for the Var. Mod?

Quantitative Proteomic Analysis of Sokotrasterol Sulfate-stimulated Primary Human Endothelial Cells
-Has data but did not publish
- Used "cICAT-13C0) or the heavy (sokotrasterol sulfate-treated, cICAT-13C9)" but I can't add super/sub script on page
- Is "D-Salt Excellulose plastic desalting column" something I shsould put in seperation technique?

Automated Yeast Two-hybrid Screening for Nuclear Receptor-interacting Proteins
-Has data but did not publish
- Did not use any Mass Spec ....not sure what this was about, actually