Powers Wiki - User contributions [en]

2D NMR Analysis (CCPNMR)

2015-08-11T22:26:56Z

Dmarshall:

==Opening Spectra==

Go to the “Project” tab and “open spectra”

Change the file format to “Bruker”

Change file type to “All”

Find the spectrum you want to open in your documents folder and choose the “proc” file

Rename the file (ex: HSQC_10)

Click on “Open Spectrum”

Reference the ppm (change the numbers)

Click on “commit” and choose “close-all done”

Repeat these steps for any other spectra that you want opened and you can overlay the spectra

* To toggle between spectra, click on the “spectra” button on the spectra window and then toggle between the spectra that you want shown

* To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window

==Peak Picking==

Hold control and shift down while clicking and dragging over area that you want peak picked

Then you can delete peaks by clicking on peak (hold shift for multiple) and right-clicking on the peak. Then click on “peak” and “delete selected”.

Click on the “Peak” tab and click “peak lists”. The peak table tab will show you the peaks that you selected on a table

==Assigning Peak Resonance==

Go to peak table and click on Assign F1. Choose “new”, then “select option”. Then “set resonance name” and name it.

Repeat for F2

If they’re the same spin system, then click “set same spin system”

Repeat “assign resonance name” for all other peaks that belong to same spin system but don’t click “set same spin system” again.

Once done, go to “resonance” tab and click on “Resonances”. Highlight all that are in same spin system and click “add to spin system”.

Click the spin system that they belong to and the software will label them as the same spin system.

Repeat for all spin systems

==Exporting Spectra==

Go to the window tab

Click on “print window”

Set your parameters

Click on “save print file”

Now you can drag and drop the file into CorelDraw or other software

==Problems Opening==

If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.

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

700 MHz NMR checklist

2015-08-11T20:53:52Z

Dmarshall:

'''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

* Name it: initials-title-date

* Experiment: zgesgp (wipes out the water peak)

* Set solvent

* Check the “getprosol” box

Lock the sample by typing “lock d2o”

* 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”

* 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.

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

* Type “pulprog” and choose “zg”

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

* Run the sample by typing “zg”

* To transform FID into spectrum, type “efp”

* Type “apk” to autophase

* 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.

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

* Type “edprosol” and set the p1 you found into both pulse widths and hit enter in each one

* Click the “copy to solvent” buton and select all relevant

* 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

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.

* Experiment for HSQC: C13HSQCS1SP2 (metab)

* Experiment for HMBC: C-13 HMBC

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

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

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

* 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 in “rga” to check the automatic receiver gain

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

* 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).

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

2D NMR Analysis (CCPNMR)

2015-08-11T20:51:35Z

Dmarshall: /* Opening Spectra */

2D NMR Analysis (CCPNMR)

2015-08-11T20:51:03Z

Dmarshall:

==Opening Spectra==

Go to the “Project” tab and “open spectra”

Change the file format to “Bruker”

Change file type to “All”

Find the spectrum you want to open in your documents folder and choose the “proc” file

Rename the file (ex: HSQC_10)

Click on “Open Spectrum”

Reference the ppm (change the numbers)

Click on “commit” and choose “close-all done”

Repeat these steps for any other spectra that you want opened and you can overlay the spectra

*To toggle between spectra, click on the “spectra” button on the spectra window and then toggle between the spectra that you want shown

*To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window

==Peak Picking==

Hold control and shift down while clicking and dragging over area that you want peak picked

Then you can delete peaks by clicking on peak (hold shift for multiple) and right-clicking on the peak. Then click on “peak” and “delete selected”.

Click on the “Peak” tab and click “peak lists”. The peak table tab will show you the peaks that you selected on a table

==Assigning Peak Resonance==

Go to peak table and click on Assign F1. Choose “new”, then “select option”. Then “set resonance name” and name it.

Repeat for F2

If they’re the same spin system, then click “set same spin system”

Repeat “assign resonance name” for all other peaks that belong to same spin system but don’t click “set same spin system” again.

Once done, go to “resonance” tab and click on “Resonances”. Highlight all that are in same spin system and click “add to spin system”.

Click the spin system that they belong to and the software will label them as the same spin system.

Repeat for all spin systems

==Exporting Spectra==

Go to the window tab

Click on “print window”

Set your parameters

Click on “save print file”

Now you can drag and drop the file into CorelDraw or other software

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

2D NMR Analysis (CCPNMR)

2015-08-11T20:49:53Z

Dmarshall:

'''Opening Spectra'''

Go to the “Project” tab and “open spectra”

Change the file format to “Bruker”

Change file type to “All”

Find the spectrum you want to open in your documents folder and choose the “proc” file

Rename the file (ex: HSQC_10)

Click on “Open Spectrum”

Reference the ppm (change the numbers)

Click on “commit” and choose “close-all done”

Repeat these steps for any other spectra that you want opened and you can overlay the spectra

*To toggle between spectra, click on the “spectra” button on the spectra window and then toggle between the spectra that you want shown

*To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window

'''Peak Picking'''

Hold control and shift down while clicking and dragging over area that you want peak picked

Then you can delete peaks by clicking on peak (hold shift for multiple) and right-clicking on the peak. Then click on “peak” and “delete selected”.

Click on the “Peak” tab and click “peak lists”. The peak table tab will show you the peaks that you selected on a table

'''Assigning Peak Resonance'''

Go to peak table and click on Assign F1. Choose “new”, then “select option”. Then “set resonance name” and name it.

Repeat for F2

If they’re the same spin system, then click “set same spin system”

Repeat “assign resonance name” for all other peaks that belong to same spin system but don’t click “set same spin system” again.

Once done, go to “resonance” tab and click on “Resonances”. Highlight all that are in same spin system and click “add to spin system”.

Click the spin system that they belong to and the software will label them as the same spin system.

Repeat for all spin systems

'''Exporting Spectra'''

Go to the window tab

Click on “print window”

Set your parameters

Click on “save print file”

Now you can drag and drop the file into CorelDraw or other software

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

2D NMR Analysis (CCPNMR)

2015-08-11T20:48:48Z

Dmarshall: Created page with "'''Opening Spectra''' Go to the “Project” tab and “open spectra” Change the file format to “Bruker” Change file type to “All” Find the spectrum you want..."

700 MHz NMR checklist

2015-08-11T19:33:01Z

Dmarshall:

'''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).

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

700 MHz NMR checklist

2015-08-11T19:30:51Z

Dmarshall:

'''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).

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

700 MHz NMR checklist

2015-08-11T19:30:10Z

Dmarshall: /* 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

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).

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

700 MHz NMR checklist

2015-08-11T19:29:37Z

Dmarshall: /* 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

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).

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

'''Check in for the NMR 700mHz'''

2015-08-11T19:23:26Z

Dmarshall: Created page with "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 elec..."

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).

700 MHz NMR checklist

2015-08-11T19:16:42Z

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..."

Making Heatmaps

2012-08-17T03:49:26Z

Dmarshall:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

data <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(data) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

Data <- data [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

Data_matrix <- data.matrix (data)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (Data_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

[[Category:Protocols]]

Category:Protocols

2012-08-16T02:22:12Z

Dmarshall: Blanked the page

Category:Protocols

2012-08-16T02:17:59Z

Dmarshall:

==Load the data==
The data can be prepared in csv or text file to load the data in to R
===Type: read.csv("your file name.csv")===
e.g data <- read.csv (“list.csv”)
==To name the rows of the heat map==
===Type: Row.names(data) <- data$Name===
==To exclude the first column from the heat map==
===Type:Data <- data [,2: n]===
where n is the number of columns to be included in the heat map
==To change the loaded data in to data matrix==
===Type: Data_matrix <- data.matrix (data)===
==To use gnuplot library==
Note: Gnuplot package must be installed in R.
===Type:library("gplots")===
==To make heat map==
===Type: heatmap.2 (Data_matrix, dendrogram="row", col= redgreen (75), scale="none", key = TRUE, keysize = 1.0, margins = c(4,30), density.info="none", trace="none")===

Water-Suppression using pre-saturation pulses (zgpr/zgcppr)

2012-02-15T23:09:16Z

Dmarshall:

==Justification==
The majority of samples we run in D2O suffer from residual H2O signal masking the actual small molecule signals. This is because the small molecule concentration is typically ~100μM unlike water which has a concentration of 55M so any residual protons which have exchanged with the D2O will overpower any small molecule signal that is not of sufficient concentration. However, we can get around this issue using water suppression methods. A low power pulse at the solvent frequency and is applied during the preparation delay. This low power pulse excites the water proton signal such that no signal can fully accumulate and be measured.
===Water-Suppression===
[[Image:Water_suppression_spectrum.png]]

The figures above displays a no water suppression zg30 spectrum compared to a water suppression zgpr spectrum respectively.

===ZGPR/ZGCPPR Pulse Sequence===
[[Image:ZGPR_ZGCPPR_pulse1.png]]

Both methods are comparable in data quality, experiment time and will suppress residual water signals. The benefit of the zgcppr pulse sequence is a more complete saturation by compensating for inhomogeneities in the applied B1 field using a series of composite 90o pulses. The result is a slightly more narrow residual water signal that must be removed during processing (zgpr: 265Hz zgcppr: 221Hz) and would be beneficial for molecules with resonances near that of water.

[[Image:ZGPR_ZGCPPR_spectrum.png]]
==Methodology==

====Finding the O1====
NOTE: The commands are for Bruker software primarily TOPSPIN.

NOTE: After any command is typed you must press enter to execute.

# We must first check where the residual water peak resonance appears in the spectrum so that we know where to apply the low power pulse to suppress the signal, this is called the O1. More generally the O1 is the center of the spectrum and is used as a reference.
# Follow steps to setup (create file, lock, shim, tune etc…) a typical 1D experiment
# Once the experiment is set up type 1H in the command line and press enter (NOTE: This will pull in the standard parameters for a typical 1D spectrum (no suppression) using the zg30 pulse sequence)
# Set number of scans (ns) to 1: Type ns and set to 1
# Set number of dummy scans (ds) to 0: Type ds and set to 0
# Set the receiver gain: Type rga (NOTE: rg should be about 10-35 check by typing rg)
# Run spectrum: Type zg
# To view FID type a
# When finished acquiring data Type efp to process
# Auto phase correct: Type apk
# Auto baseline correct: Type abs
# Move cursor over center of water peak (Very large peak ~4.5-5.0ppm) write down peak center in Hz
# Type iexpno to advance to the next experiment file
====Water Suppression Pulse ====
# Under the new experiment file: Type pulprog and enter in the experiment you want to run (zgpr/zgcppr)
# Enter the solvent that you are using (typically D2O) Type solvent
# Pull in the standard pulse parameters (i.e. pulse lengths and delays) Type gpro (NOTE: You must have the correct solvent set to enter correct parameters)
# Type O1 and enter in new O1 value in Hertz (Hz) from the above experiment
# Set receiver gain Type rga (NOTE: rg should be about 35-50 check by typing rg)
# Set initial number of scans to 1 Type ns and set to 1
# Set initial number of dummy scans to 0 Type ds and set to 0
# Set delay/pre-saturation length: Type d1 and set to 2.00seconds (WARNING: The Cryoprobe is expensive!!! We don’t want to burn out the probe by putting in too much power. When using the Cryoprobe DO NOT set d1 above 2.00seconds with a power level no greater than 50dB!!!)
# Type zg (Note: this short experiment will let you take a quick check on the quality of water suppression)
# If water suppression is acceptable (i.e. minimal water signal) set ns and ds back to desired parameters (NOTE: Typically for our runs at 100μM small molecule ns=128 and ds=16)
# Type zg

When finished running SIGN LOG BOOK.

Transfer data to workstation or onto computers in the lab with ACD software.

[[Category:Protocols]]