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General Information

Ok, this comes up from time to time. Essentially if you feel we contributed intellectually to your project it is appropriate for us to share authorship. If not, then no we should not be authors on your paper.  Usually it’s pretty  obvious what side your project falls on, but if you have any questions it’s always a good idea to talk to us about it. We don’t mind.

If you want a more detailed explanation of  authorship when using a core facility please have a look at the ABRF Authorship Guidelines. These are the community standards most core facilities follow when there are questions about authorship

 

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We are Located in Room 1414 of the Genome center.

You can use the map links below

Google Maps

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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.

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If you have any questions please do not hesitate to call

The Lab number is 530-754-9474

Amino Acid Analysis and Edman Sequencing = (530) 752-7327

Brett S. Phinney 530-754-5298

Also Find us on Twitter

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Glad you asked, we sure do. We offer pilot projects every 6 months where 3-5 projects will get funded up to 2,500 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

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

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For pictures and descriptions please see

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It varies, but is usually 5-10 days for bottom up protein ID, pull-downs… etc… We can be much quicker (2-3 days) if the samples are already digested. We will inform you if there are any delays.

Complicated projects (Label free quantitation for example) that require multiple replicates and extensive data analysis can take a very long time and probably should not be attempted by people off campus. It is always much better to do these types of experiments with your local proteomics facility. If you don’t have that option, give us a call, we still maybe able to help you.

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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)
We have been thinking about how to implement an automated system for checking the status of your samples. We haven’t had a lot of requests for this, but if it interests you, please let us know

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The building front doors 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.

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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…..The University does not allow us to keep our doors open sadly….At least they let us out from time to time!

 

 

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We offer many clases, Please see our Classes (insert link) page for more details

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Around 2006 the MSF was split into two parts. The Amino Acid Analysis and Edman sequencing moved over to the proteomics core in the Genome Center and the self use mass spectrometers from the MSF turned into the campus mass spectrometry facility.

The MSF and the Genome Center proteomics core are are essentially the same thing and occupy the same space in the Genome Center Building on campus. We maintain the MSF name and website because the Molecular Structure Facility (MSF) has been around a long time and a lot of people know our Edman and Amino Acid Analysis services through that name. We our proud that we are able to keep Edman and AAA operational (and even expanding) when most other facilities have closed them.

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Ok, this is a great question (thanks for asking!). We have a number of quality control procedures we do before and during the analysis of your sample. Every facility  will do this a bit differently, but this is how we do it. It is also evolving as new technology and software becomes available.

Digestion QC

We practice bottom up proteomics, which means that your protein sample is digested into peptides before we analyze them by LC-MS/MS. This digestion step is crucial and if it fails, nothing will work. When we digest your sample, we also digest a known control sample. Usually this is a gel piece from a gel of a human cell lysate. If your sample looks unusual or shows signs of a failed digestion (rare, but it does happen), excess keratin contamination or polymer contamination we analyze the control digestion and compare it to our historical data of that control sample. If the control digestion has failed we will contact you and apologise profusely. We will also of course not charge you. This type of failure does happen, but it is rare.

Instrumentatio QC

Nano-Scale LC-MS/MS is tricky and the sensitivity and chromatography of our machines can vary (sometimes dramatically). So how do we control for this and how do we know when our machines are performing well enough to run your samples. We have two types of controls we use for this step. The first is  replicate control runs of 125 fmol of a BSA digest. We buy this BSA digest from Michrom Bio-resources and analyze them right before we run your sample. Here is an example of a recent control run (July 2011). We then make 7 extracted ion chromatograms for 7 peptides from this digest that span the entire gradient. We look for such things as peak shape, intensity, retention time, etc..

 

We then run the same sample again and look for retention time reproducibility.


 

Finally we search the BSA QC run and look for the number of peptides identified, sequence coverage etc… We store all this data in an excel spreadsheet and currently have historical data going back several years for every LC-MS/MS system we own. So we know before we run your sample, how the machine is behaving and how it’s performance compares to past performance.

We also have a more complex QC (Human cell lysate) which we run every few weeks or when we have have a suspicion something is wrong. We do not run this sample daily because running such complex samples usually will degrade the machines performance after the run is complete, unlike our BSA control.

If you have any other questions please give us a call or send us an e-mail.

 

Last updated on July 14, 2011 by Brett S. Phinney, Ph D.

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We know there are many labs you can send you samples to (for a list please see the ABRF Core Marketplace or Science Exchange) and we appreciate you considering us for your samples. What we guarantee is that we will treat your samples like they were our own and do every test and take every precaution we can reasonably take to produce the best data for your samples. We cannot guarantee that we will give you the result you  are looking for however, as that has a lot to do with sample prep and variables that are outside our control. But I will guarantee that the personnel in the lab are always a phone call or e-mail or short walk  away and will be happy to discuss your project and samples and will work with you to solve any problems that arise. We are always here to bounce ideas off of or discuss your data (or data you obtained from elsewhere).

Don’t be shy about contacting us (seriously we like it!)

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We operate on a first come first serve queue with the following exceptions

Samples from major users of shared instrumentation grants are prioritized over non major users for that particular instrument

On campus customers are prioritized over non campus customers

Experiments that require batching or have samples that need to be run in close proximity with each other may be prioritized or de-prioritized depending on the other samples in the queue to ensure efficient operation of the equipment

The Proteomics Core has an advisory committee that provides oversight to the facility and is the appropriate group to resolve any conflicts that might arise regarding sample prioritization of on campus customers.

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Glad you asked. If you want another place to send your samples or just want a second opinion, I can recommend the following labs. They do great work. You will not be disappointed

Yale MS & Proteomics Resource

Stanford SUMS

UMASS Proteomics and Mass Spectrometry Facility

Rockefeller Proteomics Resource Center

 

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