Ben's Blog

Week 6 (6-12)

2006-06-12T17:46:00.000-07:00

A Novel, Evolutionarily Conserved Protein Phosphatase Complex Involved in Cisplatin Sensitivity
- Has data but did not publish

Analysis of Leaf Proteome after UV-B Irradiation in Maize Lines Differing in Sensitivity
- Has data but did not publish
- How would I write "modification of cysteine by polyacrylamide."

Blue Native/SDS-PAGE Analysis Reveals Reduced Expression of the mClCA3 Protein in Cystic Fibrosis Knock-out Mice
- Has data but did not publish

Development of an Internally Controlled Antibody Microarray
-Has data but did not publish
-This was not a mass spec paper

Gametes Alter the Oviductal Secretory Proteome
-Has data but did not publish

GYF Domain Proteomics Reveals Interaction Sites in Known and Novel Target Proteins
--Has data but did not publish
-This is a Yeast 2 Hybrid Study

Pooled ORF Expression Technology (POET): Using Proteomics to Screen Pools of Open Reading Frames for Protein Expression
-Has data but did not publish

Protein Complexes in the Archaeon Methanothermobacter thermautotrophicus Analyzed by Blue Native/SDS-PAGE and Mass Spectrometry
-Has data but did not publish

Proteomic Analysis of Formalin-fixed Prostate Cancer Tissue
-Has data but did not publish

Proteomic Study Reveals That Proteins Involved in Metabolic and Detoxification Pathways Are Highly Expressed in HER-2/neu-positive Breast Cancer
-Has data but did not publish

Regulation of Co-repressive Activity of and HDAC Recruitment to RIP140 by Site-specific Phosphorylation
-Has data but did not publish

Proteomics-based Identification of Human Acute Leukemia Antigens That Induce Humoral Immune Response

- Has data but did not publish

Stable Isotope Labeling of Arabidopsis thaliana Cells and Quantitative Proteomics by Mass Spectrometry

Week 5 (6-5-06)

2006-06-06T19:49:00.000-07:00

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

Week 4 (5-29)

2006-05-31T08:27:00.000-07:00

Mass Spectrometric Contributions to the Practice of Phosphorylation Site Mapping through 2003: A Literature Review
-This was a review paper. There was no data in this paper.

A Proteomic Strategy for Gaining Insights into Protein Sumoylation in Yeast
-Has data but did not publish

Double Standards in Quantitative Proteomics: Direct Comparative Assessment of Difference in Gel Electrophoresis and Metabolic Stable Isotope Labeling
-Has data but did not publish
- Is (14NH4)2SO4 an isotope label?
- Is "labeled at 0 °C in the dark for 30 min with 400 pmol of cyanine dye (Cy2, Cy3, and Cy5;" an isotope label?

A Proteomic Microarray Approach for Exploring Ligand-initiated Nuclear Hormone Receptor Pharmacology, Receptor Selectivity, and Heterodimer Functionality
-Has data but did not publish
- Does not mention what peptides were used or any modifications
- Is "fluorophore" a label?

Protein Expression Profiling of the Drosophila Fragile X Mutant Brain Reveals Up-regulation of Monoamine Synthesis
-Has data but did not publish
- Is "600 pmol of Cy2 (6-mix)" a label?

Identification of Dynamic Proteome Changes Upon Ligand Activation of Trk-Receptors Using Two-dimensional Fluorescence Difference Gel Electrophoresis and Mass Spectrometry
-Has data but did not publish
- Also used "C18- ZipTips"

Tyrosine Nitration on p65: A Novel Mechanism to Rapidly Inactivate Nuclear Factor--Has data but did not publish
- Used p65. What is this?

A Genome Wide Screening Approach for Membrane-targeted Proteins
-Has data but did not publish
-This was not a Mass Spec paper

JUNE 2005

Phosphotyrosine Proteomic Study of Interferon
-Has data but did not publish
-Is IMAC a Label? (note to self: this was also used in the Tyrosine Nitration on p65 paper)
- How do I write "methyl esterification", "aspartic and glutamic acids were set as static modifications," "phosphorylation of serine, threonine,
and tyrosine were set as variable modifications"?
-used isotopes but not sure of what it is, if it is not IMAC.

Week 3 5/22/06

2006-05-23T06:29:00.000-07:00

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

Week 2

2006-05-21T16:28:00.000-07:00

The Utility of N,N-Biotinyl Glutathione Disulfide in the Study of Protein S-Glutathiolation
-Has data but did not publish
-Is FITC a labelling technique?

Identification of the Major Site of O-Linked ß-N-Acetylglucosamine Modification in the C Terminus of Insulin Receptor Substrate-1
-Has data but did not publish
- What does "spiked with the synthetic O-GlcNAc-modified peptide" mean?
- How do I write "differential modification of Ser and Thr residues (136.2 Da) and static modifications accounting for oxidation at Cys (48 Da), Met (32 Da), and Trp (16, 32, or
48 Da) and Ser/Thr (80 Da), and differential O-GlcNAc modification of Ser/Thr (203.2 Da). SEQUEST results were filtered by Xcorr scores of 1.0, 2.0, and 2.5 for 1, 2, and 3
charge state peptides)?

I have not been able to access the ProteomeCommons website so I wrote out all fields on paper and will transfer at a later date.

Elucidation of N-Glycosylation Sites on Human Platelet Proteins
-Has data but did not publish

Identification of VCP/p97, Carboxyl Terminus of Hsp70-interacting Protein (CHIP),
-Has data but did not publish

A Novel Subtractive Antibody Phage Display Method to Discover Disease Markers*
-Has data but did not publish
- What should I put for "Serum" since there is no eVOC #?
- Does not say anything about mass spec except "subjected to MALDI-TOF mass spectrometric analysis"

Proteomic Studies of the Singapore Grouper Iridovirus*
--Has data but did not publish
-How do I write "pyroglutamation" as a var mod?

A Novel Two-dimensional Electrophoresis Technique for the Identification of Intrinsically
Unstructured Proteins
--Has data but did not publish
-Does not list the mass spec (only that it was MALDI)

Low Temperature Treatment at the Young Microspore Stage Induces Protein Changes in Rice Anthers
-Has data but did not publish

New Data Analysis and Mining Approaches Identify Unique Proteome and Transcriptome Markers of Susceptibility to Autoimmune Diabetes
-Has data but did not publish
-Used "Non-obese diabetic" mice but Ontology had diabetes mellitus or insipitus
- Didn't use any Mass Specs

Organellar Proteomics
-Has data but did not publish
-"2D Gel Electrophoresis, In-gel Protein Digestion, iTRAQ Labeling,
2D LC-MALDI, Tandem Mass Spectrometry, and Data Analysis—
These are described in detail in the Supplemental Experimental
Procedures."- Where do I get that?

Differential Modification of Phosducin Protein in Degenerating rd1 Retina Is Associated with
Constitutively Active Ca2/Calmodulin Kinase II in Rod Outer Segments*
-Has data but did not publish
-When you copy and paste from Adobe, things like accents don't paste correctly (they move from above the letter and become a new character themselves)

Automated Identification and Quantification of Protein Phosphorylation Sites by LC/MS
-Has data but did not publish

Proteins Exposed at the Adult Schistosome Surface Revealed by Biotinylation
- -Has data but did not publish
- How do I write the variable mod "modification of lysine and N-terminal residues
by the biotinylation reagents."?

The Turnover Kinetics of Major Histocompatibility Complex Peptides of Human Cancer Cells
-Has data but did not publish

An Integrated Mass Spectrometry-based Proteomic Approach: Quantitative Analysis of Tandem Affinity-
-Has data but did not publish
- Is "QSTAR XL" ESI?

Molecular Diversity in Venom from the Australian Brown Snake, Pseudonaja textilis
-Has data but did not publish

Week 2 (5-15 to 5-20)

2006-05-16T17:56:00.000-07:00

The Utility of N,N-Biotinyl Glutathione Disulfide in the Study of Protein S-Glutathiolation
-Has data but did not publish
-Is FITC a labelling technique?

Identification of the Major Site of O-Linked ß-N-Acetylglucosamine Modification in the C Terminus of Insulin Receptor Substrate-1
-Has data but did not publish
- What does "spiked with the synthetic O-GlcNAc-modified peptide" mean?
- How do I write "differential modification of Ser and Thr residues (136.2 Da) and static modifications accounting for oxidation at Cys (48 Da), Met (32 Da), and Trp (16, 32, or
48 Da) and Ser/Thr (80 Da), and differential O-GlcNAc modification of Ser/Thr (203.2 Da). SEQUEST results were filtered by Xcorr scores of 1.0, 2.0, and 2.5 for 1, 2, and 3
charge state peptides)?

I have not been able to access the ProteomeCommons website so I wrote out all fields on paper and will transfer at a later date.

Elucidation of N-Glycosylation Sites on Human Platelet Proteins
-Has data but did not publish

Identification of VCP/p97, Carboxyl Terminus of Hsp70-interacting Protein (CHIP),
-Has data but did not publish

A Novel Subtractive Antibody Phage Display Method to Discover Disease Markers*
-Has data but did not publish
- What should I put for "Serum" since there is no eVOC #?
- Does not say anything about mass spec except "subjected to MALDI-TOF mass spectrometric analysis"

Proteomic Studies of the Singapore Grouper Iridovirus*□
--Has data but did not publish
-How do I write "pyroglutamation" as a var mod?

A Novel Two-dimensional Electrophoresis Technique for the Identification of Intrinsically
Unstructured Proteins
--Has data but did not publish
-Does not list the mass spec (only that it was MALDI)

Low Temperature Treatment at the Young Microspore Stage Induces Protein Changes in Rice Anthers
-Has data but did not publish

New Data Analysis and Mining Approaches Identify Unique Proteome and Transcriptome Markers of Susceptibility to Autoimmune Diabetes
-Has data but did not publish
-Used "Non-obese diabetic" mice but Ontology had diabetes mellitus or insipitus
- Didn't use any Mass Specs

Organellar Proteomics
-Has data but did not publish
-"2D Gel Electrophoresis, In-gel Protein Digestion, iTRAQ Labeling,
2D LC-MALDI, Tandem Mass Spectrometry, and Data Analysis—
These are described in detail in the Supplemental Experimental
Procedures."- Where do I get that?

Differential Modification of Phosducin Protein in Degenerating rd1 Retina Is Associated with
Constitutively Active Ca2/Calmodulin Kinase II in Rod Outer Segments*
-Has data but did not publish
-When you copy and paste from Adobe, things like accents don't paste correctly (they move from above the letter and become a new character themselves)

Automated Identification and Quantification of Protein Phosphorylation Sites by LC/MS
-Has data but did not publish

Proteins Exposed at the Adult Schistosome Surface Revealed by Biotinylation
- -Has data but did not publish
- How do I write the variable mod "modification of lysine and N-terminal residues
by the biotinylation reagents."?

The Turnover Kinetics of Major Histocompatibility Complex Peptides of Human Cancer Cells
-Has data but did not publish

An Integrated Mass Spectrometry-based Proteomic Approach: Quantitative Analysis of Tandem Affinity-
-Has data but did not publish
- Is "QSTAR XL" ESI?

The last 2 articles for week 1

2006-05-13T14:04:00.000-07:00

Identification of Sites of Mannose 6-Phosphorylation on Lysosomal Proteins
-Has data but did not publish

Subcellular and Functional Proteomic Analysis of the Cellular Responses Induced by Helicobacter pylori
-Has data but did not publish

Getting to work

2006-05-10T15:12:00.000-07:00

I am getting to work....watch out proteins, here I come

Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured
under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach
- No email for contact (just address)
- I forget is "Submission Date" for paper or data?
- This did not use isotopes, does that mean there are no modifications (I couldn't find any)
-Assumed conventional ion trap = ESI
-Since this was not a human, did not find much on the eVOC site
- Has data but did not publish

High Expression of Antioxidant Proteins in Dendritic Cells
-Not a great summary of methods
-is [3H] Thymidine incorporation into T cells the treatment labeling?
- ZSPRAY or elctrospray capillary = ESI?
- Has data but did not publish

A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions
-Carboxyl-terminal tagging of Skp1 and Met4 was performed by a PCR-based method as
described previously (11).....Is this the modifications?
-nanoflow reverse phase LC
- what is "dedesalted offline using a C18 Ziptip"
-used Strains—Yeast strains used inthis study are all isogenic to 15Daub, bar1 ura3ns, a derivative ofBF264-15D (9) but I could only find the general "yeast" online
-Has data but did not publish

Phosphate-binding Tag, a New Tool to Visualize Phosphorylated Proteins
--Has data but did not publish
- Is IEF a method of seperation?
- No idea what was used to cleave or what organism was used

Multiplex Analysis of Intracellular Signaling Pathways in Lymphoid Cells by Microbead Suspension Arrays
- I don't think this used Mass Spec
- No published data

Microwave-assisted Protein Preparation and Enzymatic Digestion in Proteomics
- is "ion trap" ESI?

Simultaneous Qualitative and Quantitative Analysis of theEscherichia coli Proteome: A Sweet Tale
-Has data but did not publish
-low energy (MS) and elevated energy (MSE)= MS/MSE ?

Quantitative Proteomic Comparison of Rat Mitochondria from Muscle, Heart, and Liver
- Has data but did not publish
- is DTT a modification?
- Has "methionine oxidation and protein amino-terminal acetylation as variable modifications" but how do I put those in the database

Maturation of Human Neutrophil Phagosomes Includes Incorporation of Molecular Chaperones and Endoplasmic Reticulum Quality Control Machinery
- Has data but did not publish
- for the analysis is says it searched for "carbamidomethylation, modification of peptide
N-terminal glutamine to pyroglutamine, oxidation of methionine, acrylamide-modified cysteine" but doesn't mention them in the methods as modifications

Characterization of an RNA Granule from Developing Brain
- has data but did not publish
- what is Day 18 Brain for the eVOC
- variable was "oxidation (Met)"
-Difficult article to get much info from

Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data
-Has data but did not publish
-carboxyamidomethylation of cysteines and methionine oxidation as variable modifications ?

Proteomic Analysis of Bovine Brain G Protein Has data but did not publish
-Not much for information

Test Post

2006-05-09T10:47:00.000-07:00

Test