blank subtraction

[danischles]

Hi! Thank you so much for all your work on this program - it has been a huge help in my analysis of Orbitrap data.

I'm wondering if you have a recommended way to do blank subtraction of your data in preparing the mass lists to run through MFAssignR?

Just looking for suggestions or codes that others might be using...

Thanks!

[skschum]

Hello, I am glad MFAssignR has been helpful for you. Background subtraction is definitely a bit of a trick in my experience and is difficult to standardize over many samples. However there are a few methods you can use as a base for blank subtraction. I put together an r script with some examples of how I have done blank subtraction in the past. Hopefully it can be useful. Please let me know if you have any other questions. Thanks, Simeon

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On Thu, Jul 21, 2022 at 12:01 PM danischles ***@***.***> wrote: Hi! Thank you so much for all your work on this program - it has been a huge help in my analysis of Orbitrap data. I'm wondering if you have a recommended way to do blank subtraction of your data in preparing the mass lists to run through MFAssignR? Just looking for suggestions or codes that others might be using... Thanks! — Reply to this email directly, view it on GitHub <#25>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF72HFH6PQ4WRIKXJN3NFMLVVF65FANCNFSM54ILDSYA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[danischles]

Hi Simeon, Thanks for the response! I'd definitely be interested in seeing what you put together for blank subtraction and comparing with what I'd be using if you'd be willing to share! Danielle On Mon, Aug 1, 2022 at 8:25 AM Simeon Schum ***@***.***> wrote:

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Hello, I am glad MFAssignR has been helpful for you. Background subtraction is definitely a bit of a trick in my experience and is difficult to standardize over many samples. However there are a few methods you can use as a base for blank subtraction. I put together an r script with some examples of how I have done blank subtraction in the past. Hopefully it can be useful. Please let me know if you have any other questions. Thanks, Simeon On Thu, Jul 21, 2022 at 12:01 PM danischles ***@***.***> wrote: > Hi! Thank you so much for all your work on this program - it has been a > huge help in my analysis of Orbitrap data. > > I'm wondering if you have a recommended way to do blank subtraction of > your data in preparing the mass lists to run through MFAssignR? > > Just looking for suggestions or codes that others might be using... > > Thanks! > > — > Reply to this email directly, view it on GitHub > <#25>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AF72HFH6PQ4WRIKXJN3NFMLVVF65FANCNFSM54ILDSYA > > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI4U23BAP5VQZKYCMKILX53VW664DANCNFSM54ILDSYA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[skschum]

Hello, I attached the document to the previous email, though I am not sure if it can make it through the various Github screens. I have added it to the Suppplemental MFAssignR Scripts folder on the MFAssignR GitHub page. Please let me know if you have any any other questions. Thanks, Simeon

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On Tue, Aug 2, 2022 at 12:52 PM danischles ***@***.***> wrote: Hi Simeon, Thanks for the response! I'd definitely be interested in seeing what you put together for blank subtraction and comparing with what I'd be using if you'd be willing to share! Danielle On Mon, Aug 1, 2022 at 8:25 AM Simeon Schum ***@***.***> wrote: > Hello, > > I am glad MFAssignR has been helpful for you. Background subtraction is > definitely a bit of a trick in my experience and is difficult to > standardize over many samples. However there are a few methods you can use > as a base for blank subtraction. I put together an r script with some > examples of how I have done blank subtraction in the past. Hopefully it can > be useful. Please let me know if you have any other questions. > > Thanks, > Simeon > > On Thu, Jul 21, 2022 at 12:01 PM danischles ***@***.***> > wrote: > > > Hi! Thank you so much for all your work on this program - it has been a > > huge help in my analysis of Orbitrap data. > > > > I'm wondering if you have a recommended way to do blank subtraction of > > your data in preparing the mass lists to run through MFAssignR? > > > > Just looking for suggestions or codes that others might be using... > > > > Thanks! > > > > — > > Reply to this email directly, view it on GitHub > > <#25>, or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AF72HFH6PQ4WRIKXJN3NFMLVVF65FANCNFSM54ILDSYA > > > > . > > You are receiving this because you are subscribed to this thread.Message > > ID: ***@***.***> > > > > — > Reply to this email directly, view it on GitHub > <#25 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AI4U23BAP5VQZKYCMKILX53VW664DANCNFSM54ILDSYA > > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF72HFHCS37SM563H4W6FRLVXFN5BANCNFSM54ILDSYA> . You are receiving this because you commented.Message ID: ***@***.***>