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Nesvilab / IonQuant

A label free quantification tool.
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Label-based quantification parameters _ IonQuant #60

Closed CFrey-palm closed 6 days ago

CFrey-palm commented 6 days ago

Hello,

I have some questions about the use of IonQuant for label-based quantification (with SILAC or sequential isotopic labelling like in Desai 2022 article [10.1016/j.mcpro.2022.100218] samples).

  1. What does the "Re-quantify" parameter do ? Does it allow the specific search of a heavy (or light) ion from the identified light (or heavy) ion, and then the requantification the log2H/L ratio with the found intensity?
  2. Does any of the "advanced option" parameters have a control on the pairing of the light and heavy ions?
  3. Why are the "Intensity" parameters on 0 by default (in SILAC3 for example) ?

Thank you and thanks for this great software! Best.

fcyu commented 6 days ago

What does the "Re-quantify" parameter do ? Does it allow the specific search of a heavy (or light) ion from the identified light (or heavy) ion, and then the requantification the log2H/L ratio with the found intensity?

Yes, your understanding is correct.

Does any of the "advanced option" parameters have a control on the pairing of the light and heavy ions?

What kind of "control" were you referring to?

Why are the "Intensity" parameters on 0 by default (in SILAC3 for example) ?

0 means no limitation.

Best,

Fengchao

CFrey-palm commented 6 days ago

Thanks for your very quick reply.

For example, will the heavy/light pairing be searched also within the "RT tolerance (min)"? Or are the entered numbers of min scans or min isotopes also required to search the complementary heavy ion based on a light ion?

Best,

fcyu commented 6 days ago

For example, will the heavy/light pairing be searched also within the "RT tolerance (min)"?

Yes, the RT tolerance (min) controls that.

Or are the entered numbers of min scans or min isotopes also required to search the complementary heavy ion based on a light ion?

Yes, the min scans and min isotopes are applied to all detected features, including from MS/MS identification, requantified, and MBR transferred ones.

Best,

Fengchao