DeRosa:Protocols/Mass spec

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Sending DNA Samples to Novatia for MS Analysis

Step 1: Prepare the DNA Sample

- Novatia requests at least 1 nmol to obtain a satisfactory spectrum. Send around 10 nmol if possible (+signal to noise, allows optimization runs). - The sample should be desalted and dried. Although “on-line desalting” is possible by Novatia, it’s better not to rely on this. (See note at bottom for desalting) - Place the DNA tubes in a Ziploc bag with a few dry packs (the ones the amidite bottles are shipped in are convenient). Place this inside an old tip box.

Note: Steps 2-4 are done simultaneously

Step 2: The Novatia Sample Form

Customer Information: Maria DeRosa Carleton University 613-520-2600 x3844 Fax: blank Email:

Payment Information: Susa will fill this out. You can write “Susa’s Card” at the top

Check off FIA/MS for a single sample, or use the FIA/MS multiple sample submission sheet

Check off MW confirmation

Indicate your sample names, the fact that it is provided as a solid under “Sol./Liq.”, the number of nanomoles under “Wt/Vol/Conc”, the expected molecular weight (Oligocalc), and indicate any special instructions (like “protect from light”, other potential molecular weights present, etc.)

Other fields do not have to be filled out

Step 3: The Waybill

Obtain a FedEx International Air Waybill from the paper tray in 311 (or from Stores).

Fill out the fields on the waybill. Check the Novatia website for the current address.

Section 1. Date and sender’s name and phone number (Maria is the sender). Scratch out Business Centre and write “Room 118, Steacie Building”

Section 2: The account from which the MS will be paid for

Section 3: Check the Novatia website for the current address.

Section 4: Shipment Information: 6 DNA samples x 1.5 mL epitube DNA is synthetic, ~20 nanomoles Non-toxic, non-hazardous For Research Purposes Only

Value: $10 - Even if you feel your samples are worth more than $10, this value remains the same presumably for shipping insurance and/or customs reasons.

There should be 1 package, approx 1 pound, dimensions are not needed.

Section 5: FedEx International Priority

Section 6: Other

Section 8b: Sender

Section 9: Sign your name

Step 4: Inform Susa

Send an email to Susa ( declaring that you want to ship MS samples to the USA, using the template below. (Change the number of samples, quantity, waybill number etc.). This would ideally be sent the day before to ensure she gets the paperwork returned.

Shipped To: Novatia, LLC attn. Sample Submission 11 Deer Park Drive, Suite 202 Monmouth Junction, NJ 08852 Phone: 732-274-9933

Shipped From: Carleton University Maria DeRosa, Chemistry Department 1125 Colonel By Drive Ottawa, ON K1S 5B6 Phone: 613-520-2600 x 3844

Description of Goods

6 DNA samples x 1.5 mL epitube DNA is synthetic, made on a DNA synthesizer Total weight of the samples ~20 nanomoles Non-toxic, non-hazardous For Research Purposes Only No Commercial Value

Total Value: $10.00

Waybill # 8678 3312 5675

Step 5: Bring the samples, waybill, and Novatia forms to Susa

Step 6: Maria will receive the email from Novation that contains a link to the results. To access these results the login and password are:

Login: carleton Password: md0911

If you would like to view your data you can try downloading the software from Novatia. You can access it at

T:\DeRosaGroup\Shared\Novatia's MS Viewer\ProMassDecView

You click on “view data” just at the top of the web results to download the data.

Tariq’s Desalting Method: -dissolve anhydrous EDTA (not the Na salt) about 8mg per mL. -since it doesn’t not dissolve well, vortex and heat this mixture for a while -centrifuge at the maximum for 2 minutes (to allow the undissolved EDTA to settle at the bottom) -using the supersaturated supernatant, wash (with desalting tubes etc) your DNA with at least 300uL -wash with deionized water several times