Can Ion Quant perform LCF-MBR on fractionated samples? or only for single LC-MS runs?

[TeckYewLow]

Hi,

I am new to Ion Quant. I plan to apply Ion Quant to perform LFQ-MBR on samples separated into multiple fractions. In the past, match-between runs only work for single LC-MS runs. Does Ion Quant support LC-MS runs from multiple fractions?

Thank you very much!

Best,

Teck

[fcyu]

Hi Teck,

Yes, IonQuant support fractionated LFQ-MBR. We also have a pre-released version supporting fractionated isotopic labelling quant (e.g., SILAC). Please contact yufe AT umich.edu if you want to have a try.

Best,

Fengchao

[TeckYewLow]

I already sent email to yufe AT umich.edu to get a trail copy for multi-fraction LFQ-MBR! Thanks!

Best regards,

Teck Yew

On Fri, Mar 24, 2023 at 9:16 PM Fengchao @.***> wrote:

Hi Teck,

Yes, IonQuant support fractionated LFQ-MBR. We also have a pre-released version supporting fractionated isotopic labelling quant (e.g., SILAC). Please contact yufe AT umich.edu if you want to have a try.

Best,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/IonQuant/issues/39#issuecomment-1482782328, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6WRW7S6YGYXTVPOHNYPL73W5WNENANCNFSM6AAAAAAWGF6OEE . You are receiving this because you authored the thread.Message ID: @.***>

Pusat Perubatan UKM (PPUKM)

[fcyu]

I don't think I received the email. Did you replace the AT with @?

Best,

Fengchao

[TeckYewLow]

Oh I see.

I did send to these addresses yesterday from my official email address: @.***

to: @. cc: Nesvilab/IonQuant @.>, Author @.***>

The message looked like this:

Dear Fengchao,

I would like to try fractionated LFQ-MBR. How can I implement it?

Best regards,

Teck

Best regards,

Teck Yew

On Sat, Mar 25, 2023 at 12:00 PM Fengchao @.***> wrote:

I don't think I received the email. Did you replace the AT with @?

Best,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/IonQuant/issues/39#issuecomment-1483711614, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6WRW7SMCTUP6M73PJ77MSTW5ZUXRANCNFSM6AAAAAAWGF6OEE . You are receiving this because you authored the thread.Message ID: @.***>

Pusat Perubatan UKM (PPUKM)

[TeckYewLow]

Hi @fcyu

If LFQ-MBR is used to analyzed label-free, multi-fraction LC-MS runs, how dos this algorithm work? Is MBR performed on Frac1 of Experiment1 to the corresponding Frac1 of Experiment2; and Frac2 of Experiment1 to the corresponding Frac2 of Experiment2 and so on? Or Is it performed on all loaded LC-MS runs regardless of fractions?

[fcyu]

We have two parameters to control this: MBR min correlation and MBR top runs. IonQuant basically picks the "most similar" runs to transfer IDs. Details can be found from https://www.mcponline.org/article/S1535-9476(21)00050-5/fulltext

Best,

Fengchao

[TeckYewLow]

Thanks. I am new with MSFragger. I will read it up. By the way, I have send an email to request for version that enables multi-fraction LFQ-MBR but I have not received any reply yet.

Thank you very much!

[fcyu]

I did not receive the email. Could you check if the email address is correct: yufe AT umich.edu but replacing AT with @.

Best,

Fengchao

[TeckYewLow]

I have sent an email just now. I hope it won't be redirected to the spam folder.

Thank you so much!

[fcyu]

Received your email and sent the link to download.

Best,

Fengchao

[TeckYewLow]

Thank you. I received 3 files. Philosopher 5.00; IonQuant 1.94; and Fragpipe 19.2. Inside the tools folder, I do not find MSFragger. Do I copy MSFragger 3.7 into the new tools folder? Also I loaded the new IonQuant 1.94 to the Fragpipe. I can't seem to find any button in the IonQuant tab to enable multi-frac LC-MS label-free quantification?

Best,

Teck

[fcyu]

Do I copy MSFragger 3.7 into the new tools folder?

Yes, use your existing MSFragger.

I can't seem to find any button in the IonQuant tab to enable multi-frac LC-MS label-free quantification?

There is no additional button. It is supported under hood.

Best,

Fengchao

[TeckYewLow]

Thank you. So IonQuant can automatically identify the best fitting fraction (LC-MS run) within an Experiment to compare and correlate with other fitting fraction across different Experiments? I do not have to define any parameters? That is great!

[fcyu]

You are welcome.