700 MHz NMR checklist - Revision history

Wiki Administrator at 20:24, 21 July 2022

2022-07-21T20:24:22Z

← Older revision		Revision as of 20:24, 21 July 2022
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	Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).		Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).

	~~[[category:Protocols\|NMR checklist 700]]~~
	[[category:NMR_Usage\|NMR checklist 700]]		[[category:NMR_Usage\|NMR checklist 700]]

Mjeppesen: LearningSorting

2021-09-11T04:27:29Z

LearningSorting

← Older revision		Revision as of 04:27, 11 September 2021
Line 92:		Line 92:
	Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).		Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).

	[[category:Protocols\|~~Protocols~~]]		[[category:Protocols\|NMR checklist 700]]
	[[category:NMR_Usage]]		[[category:NMR_Usage\|NMR checklist 700]]

Mjeppesen: Added to Category

2021-09-11T03:32:25Z

Added to Category

← Older revision		Revision as of 03:32, 11 September 2021
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	Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).		Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).

			[[category:Protocols\|Protocols]]
			[[category:NMR_Usage]]

Jcatazaro at 15:32, 20 March 2017

2017-03-20T15:32:05Z

← Older revision		Revision as of 15:32, 20 March 2017
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	Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).		Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).

	~~[[Category:Protocols]]~~
	~~[[Category:Metabolomics]]~~

Dmarshall at 20:53, 11 August 2015

2015-08-11T20:53:52Z

Dmarshall at 19:33, 11 August 2015

2015-08-11T19:33:01Z

← Older revision		Revision as of 19:33, 11 August 2015
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	Click on the blank document icon		Click on the blank document icon

	*1. Name it: initials-title-date		1. Name it: initials-title-date
	*2. Experiment: zgesgp (wipes out the water peak)
	*3. Set solvent		2. Experiment: zgesgp (wipes out the water peak)
	*4. Check the “getprosol” box
			3. Set solvent

			4. Check the “getprosol” box

	Lock the sample by typing “lock d2o”		Lock the sample by typing “lock d2o”
	*1. The signal should be at around 75% after you lock it. If it is too low, go to BSMS, click “power” and use the scroll on the mouse to get it to around 75%, then click “standby” on BSMS to save the change.
			1. The signal should be at around 75% after you lock it. If it is too low, go to BSMS, click “power” and use the scroll on the mouse to get it to around 75%, then click “standby” on BSMS to save the change.

	Shim the sample automatically by typing “topshim”		Shim the sample automatically by typing “topshim”
	*1. If the signal is not at 75%, adjust it in the same way as before. Also you can adjust the shimming manually by going to the BSMS and clicking on “z1”, “z2”, “x”, “y”, “xy”, etc. dimensions and using the scroll on the mouse. Don’t forget to click “standby” after any changes.
			1. If the signal is not at 75%, adjust it in the same way as before. Also you can adjust the shimming manually by going to the BSMS and clicking on “z1”, “z2”, “x”, “y”, “xy”, etc. dimensions and using the scroll on the mouse. Don’t forget to click “standby” after any changes.

	Autotune the sample by typing “atma”. To manually autotune, type “atmm”.		Autotune the sample by typing “atma”. To manually autotune, type “atmm”.

	Next you need to find the 90° pulse.		Next you need to find the 90° pulse.
	*1. Type P1 and enter “8.0” in the pop-up window
	*2. Type “pulprog” and choose “zg”		1. Type P1 and enter “8.0” in the pop-up window
	*3. Type “ns 1” (number of scans=1), then type “ds 1” (dummy scans), then type “rg 1” (receiver gain).
	*4. Run the sample by typing “zg”		2. Type “pulprog” and choose “zg”
	*5. To transform FID into spectrum, type “efp”
	*6. Type “apk” to autophase		3. Type “ns 1” (number of scans=1), then type “ds 1” (dummy scans), then type “rg 1” (receiver gain).
	*7. Not type “p1”, hit enter and try different numbers (usually between 30-44), type “zg” and “efp” in order and see what number (p1) minimizes the peak the most.
	*8. Once you have found the p1 number that minimizes the peak, divide that number by 4. That number is your 90° pulse.		4. Run the sample by typing “zg”
	*9. Type “edprosol” and set the p1 you found into both pulse widths and hit enter in each one
	*10. Click the “copy to solvent” buton and select all relevant		5. To transform FID into spectrum, type “efp”
	*11. Click the “copy to probe” and select all relevant again. A popup window will ask you which cryoprobe you want to use. Choose the one that matches the cryoprobe that is in the top left corner.
	*12. Save then “select all relevant”. Click on “yes” and “ok” whenever it asks you and make sure that you calculate all pulses when it asks. Then close out.		6. Type “apk” to autophase

			7. Not type “p1”, hit enter and try different numbers (usually between 30-44), type “zg” and “efp” in order and see what number (p1) minimizes the peak the most.

			8. Once you have found the p1 number that minimizes the peak, divide that number by 4. That number is your 90° pulse.

			9. Type “edprosol” and set the p1 you found into both pulse widths and hit enter in each one
			10. Click the “copy to solvent” buton and select all relevant

			11. Click the “copy to probe” and select all relevant again. A popup window will ask you which cryoprobe you want to use. Choose the one that matches the cryoprobe that is in the top left corner.

			12. Save then “select all relevant”. Click on “yes” and “ok” whenever it asks you and make sure that you calculate all pulses when it asks. Then close out.

	To run IconNMR, type “iconnmr” and choose the automation option and enter the password		To run IconNMR, type “iconnmr” and choose the automation option and enter the password
Line 47:		Line 63:

	Type in the name of your experiment, click on the “No.” space to activate that box, choose your solvent, and choose your experiment.		Type in the name of your experiment, click on the “No.” space to activate that box, choose your solvent, and choose your experiment.
	*1. Experiment for HSQC: C13HSQCS1SP2 (metab)
	*2. Experiment for HMBC: C-13 HMBC		1. Experiment for HSQC: C13HSQCS1SP2 (metab)
	*3. Experiment for HSQC-TOCSY: SL-hsqcetf3gpml. Metab
			2. Experiment for HMBC: C-13 HMBC

			3. Experiment for HSQC-TOCSY: SL-hsqcetf3gpml. Metab


	Click on the paramters tab and choose “edit all acquisitions parameters”		Click on the paramters tab and choose “edit all acquisitions parameters”
	*1. In the TD (data points) for the H dimension enter a number that is between 1024 and 2048 although it’s usually 2048. In the C dimension enter a number that is between 64 and 256 although it’s usually 64.
	*2. In the NS (number of scans), type 32 although it can be 64 and even 128 depending on what you want.		1. In the TD (data points) for the H dimension enter a number that is between 1024 and 2048 although it’s usually 2048. In the C dimension enter a number that is between 64 and 256 although it’s usually 64.
	3. Type d1 and hit enter and input 1.5 for the relaxation time. If you are doing the HSQC-TOCSY experiment then make sure you also change the d8 (delay time) to whatever number corresponds to the right hand panel
	*4. Type in “rga” to check the automatic receiver gain		2. In the NS (number of scans), type 32 although it can be 64 and even 128 depending on what you want.
	*5. Go to automation tab and make sure that the AUNM is set to au-zgonly.
	*6. Then click on the button that says “return to iconNMR”		3. Type d1 and hit enter and input 1.5 for the relaxation time. *If you are doing the HSQC-TOCSY experiment then make sure you also change the d8 (delay time) to whatever number corresponds to the right hand panel

			4. Type in “rga” to check the automatic receiver gain

			5. Go to automation tab and make sure that the AUNM is set to au-zgonly.

			6. Then click on the button that says “return to iconNMR”

	Copy to the samples as needed. (“edit as needed” )		Copy to the samples as needed. (“edit as needed” )

Dmarshall at 19:30, 11 August 2015

2015-08-11T19:30:51Z

← Older revision		Revision as of 19:30, 11 August 2015
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	[['''Check in for the NMR 700mHz''']]		'''Check in for the NMR 700mHz'''

	Make sure the system is accessible, e.g. not being used or under maintenance		Make sure the system is accessible, e.g. not being used or under maintenance

Dmarshall: /* Check in for the NMR 700mHz */

2015-08-11T19:30:10Z

Check in for the NMR 700mHz

← Older revision		Revision as of 19:30, 11 August 2015
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	==[['''Check in for the NMR 700mHz''']]==		[['''Check in for the NMR 700mHz''']]

	Make sure the system is accessible, e.g. not being used or under maintenance		Make sure the system is accessible, e.g. not being used or under maintenance

Dmarshall: /* Check in for the NMR 700mHz */

2015-08-11T19:29:37Z

Check in for the NMR 700mHz

← Older revision		Revision as of 19:29, 11 August 2015
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	Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).		Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).

			[[Category:Protocols]]
			[[Category:Metabolomics]]

Dmarshall: Created page with "=='''Check in for the NMR 700mHz'''== Make sure the system is accessible, e.g. not being used or under maintenance Check your belongings on your body and remove anything..."

2015-08-11T19:16:42Z

Created page with "=='''Check in for the NMR 700mHz'''== Make sure the system is accessible, e.g. not being used or under maintenance Check your belongings on your body and remove anything..."

New page

==[['''Check in for the NMR 700mHz''']]==

Make sure the system is accessible, e.g. not being used or under maintenance

Check your belongings on your body and remove anything with ferromagnetic properties such as electronic devices and keep them away from the probe

Go to the Sample Jet and change the operating mode to 5mm shuttle, then load the rack of NMR tubes.

Login to the computer

Start topspin software

Load sample by typing in “sx 101” (or if in rack 2: “sx 201”, etc)

Click on the blank document icon

*1. Name it: initials-title-date
*2. Experiment: zgesgp (wipes out the water peak)
*3. Set solvent
*4. Check the “getprosol” box

Lock the sample by typing “lock d2o”
*1. The signal should be at around 75% after you lock it. If it is too low, go to BSMS, click “power” and use the scroll on the mouse to get it to around 75%, then click “standby” on BSMS to save the change.

Shim the sample automatically by typing “topshim”
*1. If the signal is not at 75%, adjust it in the same way as before. Also you can adjust the shimming manually by going to the BSMS and clicking on “z1”, “z2”, “x”, “y”, “xy”, etc. dimensions and using the scroll on the mouse. Don’t forget to click “standby” after any changes.

Autotune the sample by typing “atma”. To manually autotune, type “atmm”.

Next you need to find the 90° pulse.
*1. Type P1 and enter “8.0” in the pop-up window
*2. Type “pulprog” and choose “zg”
*3. Type “ns 1” (number of scans=1), then type “ds 1” (dummy scans), then type “rg 1” (receiver gain).
*4. Run the sample by typing “zg”
*5. To transform FID into spectrum, type “efp”
*6. Type “apk” to autophase
*7. Not type “p1”, hit enter and try different numbers (usually between 30-44), type “zg” and “efp” in order and see what number (p1) minimizes the peak the most.
*8. Once you have found the p1 number that minimizes the peak, divide that number by 4. That number is your 90° pulse.
*9. Type “edprosol” and set the p1 you found into both pulse widths and hit enter in each one
*10. Click the “copy to solvent” buton and select all relevant
*11. Click the “copy to probe” and select all relevant again. A popup window will ask you which cryoprobe you want to use. Choose the one that matches the cryoprobe that is in the top left corner.
*12. Save then “select all relevant”. Click on “yes” and “ok” whenever it asks you and make sure that you calculate all pulses when it asks. Then close out.

To run IconNMR, type “iconnmr” and choose the automation option and enter the password

Go to the holder that your sample is in. For example if your sample is in the 1st rack and is in the first slot in that rack, then go to A1-101.

Type in the name of your experiment, click on the “No.” space to activate that box, choose your solvent, and choose your experiment.
*1. Experiment for HSQC: C13HSQCS1SP2 (metab)
*2. Experiment for HMBC: C-13 HMBC
*3. Experiment for HSQC-TOCSY: SL-hsqcetf3gpml. Metab

Click on the paramters tab and choose “edit all acquisitions parameters”
*1. In the TD (data points) for the H dimension enter a number that is between 1024 and 2048 although it’s usually 2048. In the C dimension enter a number that is between 64 and 256 although it’s usually 64.
*2. In the NS (number of scans), type 32 although it can be 64 and even 128 depending on what you want.
*3. Type d1 and hit enter and input 1.5 for the relaxation time. *If you are doing the HSQC-TOCSY experiment then make sure you also change the d8 (delay time) to whatever number corresponds to the right hand panel
*4. Type in “rga” to check the automatic receiver gain
*5. Go to automation tab and make sure that the AUNM is set to au-zgonly.
*6. Then click on the button that says “return to iconNMR”

Copy to the samples as needed. (“edit as needed” )

Highlight all of the samples and click submit

Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).

← Older revision		Revision as of 20:53, 11 August 2015
Line 15:		Line 15:
	Click on the blank document icon		Click on the blank document icon

	1. Name it: initials-title-date		* Name it: initials-title-date

	2. Experiment: zgesgp (wipes out the water peak)		* Experiment: zgesgp (wipes out the water peak)

	3. Set solvent		* Set solvent

	4. Check the “getprosol” box		* Check the “getprosol” box

	Lock the sample by typing “lock d2o”		Lock the sample by typing “lock d2o”

	1. The signal should be at around 75% after you lock it. If it is too low, go to BSMS, click “power” and use the scroll on the mouse to get it to around 75%, then click “standby” on BSMS to save the change.		* The signal should be at around 75% after you lock it. If it is too low, go to BSMS, click “power” and use the scroll on the mouse to get it to around 75%, then click “standby” on BSMS to save the change.

	Shim the sample automatically by typing “topshim”		Shim the sample automatically by typing “topshim”

	1. If the signal is not at 75%, adjust it in the same way as before. Also you can adjust the shimming manually by going to the BSMS and clicking on “z1”, “z2”, “x”, “y”, “xy”, etc. dimensions and using the scroll on the mouse. Don’t forget to click “standby” after any changes.		* If the signal is not at 75%, adjust it in the same way as before. Also you can adjust the shimming manually by going to the BSMS and clicking on “z1”, “z2”, “x”, “y”, “xy”, etc. dimensions and using the scroll on the mouse. Don’t forget to click “standby” after any changes.

	Autotune the sample by typing “atma”. To manually autotune, type “atmm”.		Autotune the sample by typing “atma”. To manually autotune, type “atmm”.
Line 35:		Line 35:
	Next you need to find the 90° pulse.		Next you need to find the 90° pulse.

	1. Type P1 and enter “8.0” in the pop-up window		* Type P1 and enter “8.0” in the pop-up window

	2. Type “pulprog” and choose “zg”		* Type “pulprog” and choose “zg”

	3. Type “ns 1” (number of scans=1), then type “ds 1” (dummy scans), then type “rg 1” (receiver gain).		* Type “ns 1” (number of scans=1), then type “ds 1” (dummy scans), then type “rg 1” (receiver gain).

	4. Run the sample by typing “zg”		* Run the sample by typing “zg”

	5. To transform FID into spectrum, type “efp”		* To transform FID into spectrum, type “efp”

	6. Type “apk” to autophase		* Type “apk” to autophase

	7. Not type “p1”, hit enter and try different numbers (usually between 30-44), type “zg” and “efp” in order and see what number (p1) minimizes the peak the most.		* Not type “p1”, hit enter and try different numbers (usually between 30-44), type “zg” and “efp” in order and see what number (p1) minimizes the peak the most.

	8. Once you have found the p1 number that minimizes the peak, divide that number by 4. That number is your 90° pulse.		* Once you have found the p1 number that minimizes the peak, divide that number by 4. That number is your 90° pulse.

	9. Type “edprosol” and set the p1 you found into both pulse widths and hit enter in each one		* Type “edprosol” and set the p1 you found into both pulse widths and hit enter in each one
	~~10. Click the “copy to solvent” buton and select all relevant~~

	~~11.~~ Click the “copy to ~~probe”~~ and select all relevant ~~again. A popup window will ask you which cryoprobe you want to use. Choose the one that matches the cryoprobe that is in the top left corner.~~		* Click the “copy to solvent” buton and select all relevant

	12. Save then “select all relevant”. Click on “yes” and “ok” whenever it asks you and make sure that you calculate all pulses when it asks. Then close out.		* Click the “copy to probe” and select all relevant again. A popup window will ask you which cryoprobe you want to use. Choose the one that matches the cryoprobe that is in the top left corner.

			* Save then “select all relevant”. Click on “yes” and “ok” whenever it asks you and make sure that you calculate all pulses when it asks. Then close out.

	To run IconNMR, type “iconnmr” and choose the automation option and enter the password		To run IconNMR, type “iconnmr” and choose the automation option and enter the password
Line 64:		Line 65:
	Type in the name of your experiment, click on the “No.” space to activate that box, choose your solvent, and choose your experiment.		Type in the name of your experiment, click on the “No.” space to activate that box, choose your solvent, and choose your experiment.

	1. Experiment for HSQC: C13HSQCS1SP2 (metab)		* Experiment for HSQC: C13HSQCS1SP2 (metab)

	2. Experiment for HMBC: C-13 HMBC		* Experiment for HMBC: C-13 HMBC

	3. Experiment for HSQC-TOCSY: SL-hsqcetf3gpml. Metab		* Experiment for HSQC-TOCSY: SL-hsqcetf3gpml. Metab


	Click on the paramters tab and choose “edit all acquisitions parameters”		Click on the paramters tab and choose “edit all acquisitions parameters”

	1. In the TD (data points) for the H dimension enter a number that is between 1024 and 2048 although it’s usually 2048. In the C dimension enter a number that is between 64 and 256 although it’s usually 64.		* In the TD (data points) for the H dimension enter a number that is between 1024 and 2048 although it’s usually 2048. In the C dimension enter a number that is between 64 and 256 although it’s usually 64.

	2. In the NS (number of scans), type 32 although it can be 64 and even 128 depending on what you want.		* In the NS (number of scans), type 32 although it can be 64 and even 128 depending on what you want.

	3. Type d1 and hit enter and input 1.5 for the relaxation time. *If you are doing the HSQC-TOCSY experiment then make sure you also change the d8 (delay time) to whatever number corresponds to the right hand panel		* Type d1 and hit enter and input 1.5 for the relaxation time. *If you are doing the HSQC-TOCSY experiment then make sure you also change the d8 (delay time) to whatever number corresponds to the right hand panel

	4. Type in “rga” to check the automatic receiver gain		* Type in “rga” to check the automatic receiver gain

	~~5. Go~~ to automation tab and make sure that the AUNM is set to au-zgonly.		* to automation tab and make sure that the AUNM is set to au-zgonly.

	6. Then click on the button that says “return to iconNMR”		* Then click on the button that says “return to iconNMR”

	Copy to the samples as needed. (“edit as needed” )		Copy to the samples as needed. (“edit as needed” )