Re: [ccp4bb] Isothermal titration calorimetry
This might have changed, but in the past file formats were different. Microcal files are text, while TA's are binary. I do have the actual description of TA's format if anyone is interested, but it must be easier to use native text export than write a converter. Original message From: Bosch, Juergen jubo...@jhsph.edu Date: To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry Hi George, this is probably a very stupid suggestion and you likely have tried it, but I'll suggest the obvious nevertheless. What happens to your .nitc file when you rename it to .itc can you read it in Origin then ? Jürgen On Mar 24, 2013, at 6:39 AM, George Kontopidis wrote: Chris, indeed nanoITC instrument analysis software is very robust and user friendly (probable more friendly than microcal, GE). Although when you need to subtract Q (heat) values (from 2 or 3 blank experiments) from your experimental data you cannot. NanoITC software can subtract Q values only from 1 blank experiment. Also if you want to present your data in a form of heat/mol in Y (vertical) axes again you cannot. It presents data in Y axes only in form of heat/injection. If you have found a way to extract 2 or 3 blank experiments from experimental data or present data in form of heat/mol, please let me know it will be very useful. The main problem in the output files from nanoITC come with an extension .nitc, by default. Unfortunately Origin (that can do all the above) can read only, filenames with an extension .itc Cheers, George -Original Message- From: Colbert, Christopher [mailto:christopher.colb...@ndsu.edu] Sent: Saturday, March 23, 2013 5:56 PM To: George Kontopidis; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry George, would you please explain your comments? We've found the TA Instruments analysis software very robust and user friendly. We have the low volume nanoITC from TA instruments and get equivalent #'s in our comparison tests to the Microcal instrument. Cheers, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 On 3/23/13 8:47 AM, George Kontopidis gkontopi...@vet.uth.gr wrote: Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23, 2013 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http
Re: [ccp4bb] Isothermal titration calorimetry
Chris, indeed nanoITC instrument analysis software is very robust and user friendly (probable more friendly than microcal, GE). Although when you need to subtract Q (heat) values (from 2 or 3 blank experiments) from your experimental data you cannot. NanoITC software can subtract Q values only from 1 blank experiment. Also if you want to present your data in a form of heat/mol in Y (vertical) axes again you cannot. It presents data in Y axes only in form of heat/injection. If you have found a way to extract 2 or 3 blank experiments from experimental data or present data in form of heat/mol, please let me know it will be very useful. The main problem in the output files from nanoITC come with an extension .nitc, by default. Unfortunately Origin (that can do all the above) can read only, filenames with an extension .itc Cheers, George -Original Message- From: Colbert, Christopher [mailto:christopher.colb...@ndsu.edu] Sent: Saturday, March 23, 2013 5:56 PM To: George Kontopidis; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry George, would you please explain your comments? We've found the TA Instruments analysis software very robust and user friendly. We have the low volume nanoITC from TA instruments and get equivalent #'s in our comparison tests to the Microcal instrument. Cheers, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 On 3/23/13 8:47 AM, George Kontopidis gkontopi...@vet.uth.gr wrote: Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23, 2013 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] Isothermal titration calorimetry
Hi George, this is probably a very stupid suggestion and you likely have tried it, but I'll suggest the obvious nevertheless. What happens to your .nitc file when you rename it to .itc can you read it in Origin then ? Jürgen On Mar 24, 2013, at 6:39 AM, George Kontopidis wrote: Chris, indeed nanoITC instrument analysis software is very robust and user friendly (probable more friendly than microcal, GE). Although when you need to subtract Q (heat) values (from 2 or 3 blank experiments) from your experimental data you cannot. NanoITC software can subtract Q values only from 1 blank experiment. Also if you want to present your data in a form of heat/mol in Y (vertical) axes again you cannot. It presents data in Y axes only in form of heat/injection. If you have found a way to extract 2 or 3 blank experiments from experimental data or present data in form of heat/mol, please let me know it will be very useful. The main problem in the output files from nanoITC come with an extension .nitc, by default. Unfortunately Origin (that can do all the above) can read only, filenames with an extension .itc Cheers, George -Original Message- From: Colbert, Christopher [mailto:christopher.colb...@ndsu.edu] Sent: Saturday, March 23, 2013 5:56 PM To: George Kontopidis; CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry George, would you please explain your comments? We've found the TA Instruments analysis software very robust and user friendly. We have the low volume nanoITC from TA instruments and get equivalent #'s in our comparison tests to the Microcal instrument. Cheers, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 On 3/23/13 8:47 AM, George Kontopidis gkontopi...@vet.uth.grmailto:gkontopi...@vet.uth.gr wrote: Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23, 2013 12:46 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.commailto:johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.commailto:shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
[ccp4bb] Isothermal titration calorimetry
Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] Isothermal titration calorimetry
I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] Isothermal titration calorimetry
It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] Isothermal titration calorimetry
Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23, 2013 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] Isothermal titration calorimetry
George, would you please explain your comments? We've found the TA Instruments analysis software very robust and user friendly. We have the low volume nanoITC from TA instruments and get equivalent #'s in our comparison tests to the Microcal instrument. Cheers, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 On 3/23/13 8:47 AM, George Kontopidis gkontopi...@vet.uth.gr wrote: Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23, 2013 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
