Nick Shulman responded: |
2015-01-12 23:33 |
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claire wu responded: |
2015-01-12 23:48 |
Dear Nick,
Thanks for the prompt reply. I have tried the "rescore" but it still dose not work. Please let me know if you have further suggestions for this. Thanks so much.
Claire |
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Nick Shulman responded: |
2015-01-13 00:43 |
Thanks for sending me your data files.
You have an SRM experiment, which means that the machine only collected for the masses that were specified ahead of time.
I believe that in order to use decoys in an SRM experiment, the decoy peptides need to be added to the instrument method before the data is collected.
What you are seeing is that there really are no chromotograms in the data file for those decoy peptides. |
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claire wu responded: |
2015-01-13 01:04 |
Dear Nick,
Thanks so much for spending time checking my data. Is there other way that I can calculate the FDR since now the big data has been generated without adding the decoy peptides?
Best,
Claire |
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Brendan MacLean responded: |
2015-01-13 06:37 |
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claire wu responded: |
2015-01-13 07:13 |
Hi, Bredan
I just found the tutorial and decided to use second-best peaks. It's good to receive the confirmation from you. Thanks so much for all the help and support from you and Nick.
Best
Claire |
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