Ionomics Recharge Facility Guidelines/FAQs

***PLEASE CONTACT US FOR THE LATEST PER SAMPLE PRICING***

 

What is Ionomics?

High throughput elemental profiling. In this facility, we use an inductively coupled plasma-mass spectrometer to measure the levels of 21 elements in a given sample: : B, Na, Mg, Al, P, S, K, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Mo, Cd, and Li.

What is the USDA-ARS/Danforth Center Ionomics facility?

The ionomics facility is a collaboration between USDA-ARS and the Donald Danforth Plant Science Center. It was built to analyze samples for the lab of Ivan Baxter, USDA-ARS Research Computational Biologist and Adjunct Associate Member at the Danforth Center. Through improvements in sample processing and instrumentation, the facility can now analyze over 1700 samples a week, and frequently has excess capacity. Due to the high demand for elemental profiling in the plant community, we have set up a recharge facility to allow other researchers to take advantage of that capacity.  

 

The facility is setup to analyze plant samples, such as seeds and leaves. It can analyze other types of biological samples, but they need to be able to fit within our analysis framework.

How fast can I get data from my analysis done?

At any given time, we usually have 1-2 months worth of samples on hand and we try to turn samples around in that time. However, occasionally we have longer queues due to machine down time and larger projects. As such we can’t guarantee a specific turnaround time. If you have a time sensitive analysis project, please let us know ASAP and we will see if we can accomplish that turnaround.

Sample Preparation

The key part of the sample preparation is getting a known amount of  the sample into our digestion tubes.  If your sample can be easily transferred into our tubes without risking any loss, you can send us pre-weighed samples. Otherwise we need to weigh the sample in the tube.

 

Any sample handling and preparation needs to be done with the idea that it is incredibly easy to contaminate samples. Even a small speck of dust or metal shaving is more than enough to contaminate a sample. As a result, we recommend that preparations that rely on metal on metal contact (scissors, for example) be avoided. That doesn’t mean that you can’t send us tissue that has been exposed to metal on metal, it just means you have to account for the potential that there may be contaminants that need to be accounted for with outlier removal or other methods. We have run samples that were combine harvested, for example, and gotten good data, but we prefer to analyze 3+ seeds in that case so that we can easily identify outliers at the packet level.

Seeds

We are able to use our weighing robot to weigh seeds that are between 50mg and 300mg. Send us approximately 10 seeds per line sorted into coin envelopes. Please let us know how many seeds per packet we should analyze.

 

If you have smaller seeds, we usually try to pool several seeds into a single sample and weigh the resulting sample, recording both the weight and the number of seeds.

Leaves/Small and large seeds/Powders

We will hand weigh leaf, small/large seed or powder samples. Whole leaves can be folded and laid flat in coin envelopes. Powder can be in eppendorf or 15mL falcon tubes. Ideally, send at least 250mg of tissue. If the leaves are smaller than 250mg, we can digest the whole leaf, if desired, otherwise we will crush the leaf and subsample to the amount we use for a standard analysis (75mg). For samples where obtaining 75mg of tissue isn’t possible, please email us and we can make other arrangements to run the samples.

Soil

Soil samples should be crushed to a fine particulate so fragments are less than 2mm in diameter. You can send us 1 gram of soil in 15mL falcon tubes and we will aliquot the amount necessary for our analysis.

Arabidopsis Analysis

 

We hope to have an Arabidopsis pipeline that will include growing the plants available this year.

Where/how should I send my samples?

The first step is to email Dr. Greg Ziegler at gziegler@danforthcenter.org with a brief description of what you would like to send us.

 

Samples should be shipped dry to us at:

Shipping Address:

Send samples to:

℅ Melissa Jurkowski

Baxter Lab

Danforth Center

975 N Warson Rd.

St. Louis, Mo 63132

 

How should I label my samples?

 

Samples should be clearly labeled, with a unique alphanumeric identifier with no spaces. Barcodes (Code 128 or QR-code) should be used where possible or if sending a large number of samples.

 

Send us a spreadsheet, with, at minimum, a column of the sample IDs being sent. Other metadata about the samples can be included as well. We will use this to verify we are recording the correct IDs and to verify that we have run all of the samples received in a shipment.

 

What happens to leftover samples?

 

Elemental analysis is a destructive process and you shouldn’t expect to receive samples sent to us back. If you would like unused tissue samples returned, please let us know and we can make arrangements to keep and return any undigested sample that remains after our analysis.

 

Ionomics Data File

 

The output of our analysis is a spreadsheet with the weight-normalized elemental concentrations (in mg analyte/kg sample).  One row per sample, metadata about run parameters, and 20 columns, one for each of the elements we measure: B, Na, Mg, Al, P, S, K, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Mo, Cd.

 

Sample analysis is performed at one dilution that has been selected to put most elements within the linear range of the machine and above the limits of detection.  However, no guarantee can be made that for all samples and all elements this threshold can be met.  Results will be reported corrected for machine drift and normalized for starting sample weight in mg/kg units, no further analysis of the data will be performed.

 

Other elements, specific isotopes, diverse sample types

 

We are able to maintain a low-cost, high-throughput elemental profiling platform by subjecting all samples to a very similar preparation and measurement process. As such, it is difficult to make specific adjustments to the system. In rare cases, we may be able to accommodate additional isotope/element measurements, but it will depend upon pipeline demand and availability of matching reference standards.
 

Can you run samples as part of a collaboration or in exchange for authorship?

We occasionally get asked if we can run samples as a collaboration, instead of as a recharge.

Unfortunately, we do not have core funds that can be used to run samples as a free service. All of our funds need to be used to analyze samples related to our project. Even in formal collaborations, collaborators frequently contribute some or all of the funds necessary to run the samples. If you think that the samples you wish to run could be useful for some of the projects described on the lab website or in our publications, please contact Dr. Baxter.

 

In terms of inclusion on publications, our general rule is that if we are just running samples and sending the data, that doesn’t merit inclusion on author lists, but we ask that you mention us in the acknowledgements. If we are helping with the downstream and analysis, making figures etc, then we probably move onto the author lists. Who paid for the sample should have no bearing on authorship.

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© 2014 By Melissa Jurkowski, using WIX

 

*Corn picture = http://capl.washjeff.edu/browseresults.php?langID=2&photoID=5107&size=l

*Soybean picture = http://en.wikipedia.org/wiki/Soybean

*Setaria picture = http://pl.wikipedia.org/wiki/Włośnica_zielona

*Plasma picture = http://plaza.ufl.edu/kamenov/kamenov.htm

 

 

 

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