We are Located in Room 1414 of the Genome center. 

You can use the map links below

Google Maps - UC Davis Genome Center

 UC Davis Maps

We are in the bottom left corner or search for the Genome and Biomedical Science Building/Facility (GBSF).

We recommend always contacting us before you ship samples.

Please send samples to


Proteomics Core, Room 1414 
Genome and Biomedical Sciences Facility 
451 East Health Sciences Drive 
Davis, CA 95616-8816 

Al also recommend shipping samples overnight and retaining the Tracking ID.

If you have any questions please do not hesitate to call
The Lab number is 530-754-9474
Brett S. Phinney 530-754-5298

 

UC Davis Genome Center Proteomics Core Rates

Effective as of August 2008

Protein Identification

This includes

·         a quality control run at 125 fmol

·         Proteolytic digestion (Trypsin)

·         database search

·         results returned via Scaffold (http://www.proteomesoftware.com )

 

Ion trap                  (LTQ)

LC/MS/MS (30-90 minute run based on complexity of your sample)         152.00

LC/LC/MS/MS (mudpit 8 x 20 minute runs)                                                          254.00

LC/LC/MS/MS (mudpit 8 x 90 minute runs)                                                          358.00

 

FTMS     (LTQ-FT)

 LC/MS/MS (30-90 minute run based on complexity of your sample)         179.00

LC/LC/MS/MS (mudpit 8 x 20 minute runs)                                                          296.00

LC/LC/MS/MS (mudpit 8 x 90 minute runs)                                                          399.00

 

^*If you perform the digest, subtract 26.00 from the above prices

 

LC/MS/MS ONLY (no data analysis, mzXML file will be returned to customer, does not include sample prep. Recommended only for people that have experience interpreting LC/MS/MS data)

LTQ or LTQ-FT  (30-90 minute run)                                                                            70.00

 

 

Targeted Proteomics (includes digest, usually 3-4 hours of data analysis are also required. Targeted proteomics projects are usually considered collaborative as designing the experiment is critical for success. Please contact us for details.

TSQ Vantage LC/MS/MS                                                                                                               152.00

 

Data Analysis/Labor Rate                                                                                             68.00/hour

 

Other Sample Prep

Costs of Reagents             +            68.00/hour

 

Things to keep in mind:

Quantitiave experiments usually require multiple runs plus considerable Data analysis time. Please contact us for specific details.

If you want to do a collaborative project with the Facility please contact us. Collaborative Projects are projects where we contribute significantly on large projects. This is recommended if you plan on doing things more complicated than simple proteins identification.  For more information please see

http://proteomics.ucdavis.edu/modules/xoopsfaq/index.php?cat_id=1#q19

and

http://proteomics.ucdavis.edu/uploads/services_vs_projects_at_the_uc_davis_proteomics_facility.pdf

 

 

 

Rates for non-profit institutions and Other Universities add 52.00%

Rates for commercial companies add 81.50%

                

 

Actually we think we are rather inexpensive for the quality of services we perform. 

For a list of other facilities around the world that offer similar services please see the ABRF yellow pages.

http://www.abrf.org/index.cfm/dir.yp

 

I'd rather phrase it as inexpensive. Since we perform lots and lots of protein ID work, we can offer this at a relatively good price. Larger projects can get quite expensive however (PTM and Label free quantitation for example)

These were adapted from the NYU Protein Analysis Facility. 
Link = http://saturn.med.nyu.edu/facilities/paf/


Policies on User Fees, Authorship and Collaboration

The UC Davis Genome Center Proteomics Facility does have some funds specifically designated to support collaborative work. These Funds are awarded twice yearly and consist of 2,000 grants. For More information please see to Brett Phinney. To support its operation the facility must rely heavily on charges from labs who use the services and who do have funding to support the research. For this reason, all investigators must arrange payment via DAFIS (UC Davis investigators), IOC (UC Campuses) or Purchase Order (non-UC) before submitting samples to the facility. We suggest that users of the facility include the costs of protein analysis in any grant proposals involving such research. A list of user fees can be found on the facility web site, and the facility director (Brett Phinney) will be happy to provide a letter of collaboration for these grant proposals. We regret any inconvenience this may cause to our colleagues, but our financial realities permit no alternatives to this policy.

Acknowledgment and Authorship 

We at the UC Davis Genome Center Proteomics Facility follow the guidelines established by the International Committee of Medical Journal Editors and similar organizations as discussed by Huth (Huth, E. J. [1986] Guidelines on Authorship of Medical Papers, Annals Int. Med. 104 : 269-274) and Bailey (Bailey, B. J. [2001] What Is an Author? Otolaryngol. Head Neck Surg. 124 :2-3 ). In general, these guidelines suggest that if scientists from the facility have helped to design or conceive the experiments, have done data analysis and interpretation of data, or both, they should be coauthors of papers that use data generated by the facility. In this case facility scientists should participate in drafting the paper or revising it for critically important content, and give final approval of the version to be published. Characterization of some posttranslational modifications on proteins, quantitative proteomics, and in some cases, extensive de novo sequencing of peptides followed by multiple protein identifications by homology searching are not routine, generally require extensive data interpretation, and in most cases constitute contributions meriting co-authorship. Simple acquisitions of mass spectra or routine protein identifications alone normally do not merit co-authorship but should be acknowledged (see below). If you are uncertain about co-authorship or have any questions or concerns about this, please discuss this issue with the facility director (Brett Phinney) before submitting your samples for analysis.
If data from the UC Davis Genome Center Proteomics Facility is used in a publication and facility scientists are not coauthors, please acknowledge the facility in the Acknowledgments section of the publication. Please send us a reprint of the paper, or an e-mail including the reference information for the publication. This helps the facility obtain funding to keep user fees lower than they would be without this funding.

Collaboration 

If a project requires extensive mass spectrometry analysis, in some cases a collaboration between the UC Davis Genome Center Proteomics Facility and another lab may be established. Collaborations usually entail co-authorship, especially when numerous analyses of a similar nature must be carried out. In all cases, collaborations can only be established by mutual agreement of the heads the labs involved, including the director of the UC Davis Genome Center Proteomics Facility (Brett Phinney). The UC Davis Genome Center has instituted Collaborative Project fees. For more information on these Please see http://proteomics.ucdavis.edu/index.php?option=com_rubberdoc&view=doc&id=41&format=raw&Itemid=8

Brett Phinney
UC Davis Genome Center Proteomics Facility 
August 22,2007

Glad you asked, we sure do. We offer pilot projects every 6 months where 3-5 projects will get funded up to 2,000 dollars. These are mainly for risky projects or groups on campus that want to try out the technology but are a little wary. 

For more information please call

Yes, we certainly do, and we are relatively inexpensive and have a decent turn-around time Please contact us for details.

We have lots of state-of-the-art instrumentation to carry out your analyses.

 

Please see

 

http://proteomics.ucdavis.edu/index.php?option=com_simplelists&view=simplelist&layout=toggle&category_id=6&Itemid=6#

 

For more information

 

 

Yes We we offer 

ITRAQ labeling and analysis
label free quantitation using our LTQ-FT and the Thermo-Electron software SIEVE
AQUA Stable Isotope quantitation

These can get quite expensive unfortunately

It varies, but is usually 5-10 days. We can be much quicker (2-3 days) if the samples are already digested. We will inform you if there are any delayed.

 

 

Our facility rule is that someone will be in contact with you at least every three days to update you on the status of your samples. If you don't hear from us in three days, please call and complain (loudly if you'd like)

Very good question. The building front doors (by the Cafe) are open in the morning during business hours. After 5 pm please give us a call at 754-9474 and we will come and let you in.

Another very good question. We now have a doorbell at the entrance to 1414 GBSF. Give us a ring and we'll come out to let you in.....

We offer classes every Tuesday... if we get at least three people sign up for them

Please call the lab and have your name put on the list. When we get three people signed up, we will e-mail you. If you would like to see any additional classes please send us a note

In addition every summer we offer an intense 1 week proteomic short course. For details please see the UC Davis biotechnology program

http://www.biotech.ucdavis.edu/