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PNNL-Comp-Mass-Spec / Informed-Proteomics

Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
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"An item with the same key has already been added" #8

Open grocklin opened 6 years ago

grocklin commented 6 years ago

Hello,

I'm trying to run PbfGen on this mzML file, and getting the error "An item with the same key has already been added". Could you help me understand why and how I might fix this?

https://www.dropbox.com/s/9y1of85g5ju9252/091817_mix3_dda_20min.mzML?dl=0

I created the mzML file using MSConvert from Waters RAW format.

Thanks, Gabriel

alchemistmatt commented 6 years ago

Thank you for providing the .mzML file. We will look into this

FarmGeek4Life commented 6 years ago

This has to do with a conflict between how scans are referenced internally, and the waters function:scan id format. Internally (because this was originally written with a focus on Thermo .raw data) we reference the scans using an integer, and so working with Waters data with duplicate scan numbers with different functions is problematic, as least in setting up the internal references to individual scans. There are several options for compensating for this, but I don't know enough about waters functions/scans to choose one that will reasonably represent the data file. I can see that your data has 4 functions, where functions 1 and 4 are MS1, and functions 2 and 3 are MS2. Can you give us more information about the 4 functions? Also, I noticed that it is IMS (or TW-IMS) data; you are venturing into uncharted territory with MSPathFinder...

grocklin commented 6 years ago

Hi, thanks for looking at this and replying. I believe the four channels are-

1: Full scan MS (with ion mobility) 2: MS/MS of the 1st selected precursor (with ion mobility) 2: MS/MS of the 2nd selected precursor (with ion mobility) 3: MS scan of the lock mass channel (no ion mobility, or at least not one that is usable.) (not relevant)

If this is uncharted territory, do you think it will ultimately be doable? Is there other information (maybe we could ask Waters) that would help?

Thanks, Gabe

On Mon, Nov 6, 2017 at 12:20 PM, Bryson Gibbons notifications@github.com wrote:

This has to do with a conflict between how scans are referenced internally, and the waters function:scan id format. Internally (because this was originally written with a focus on Thermo .raw data) we reference the scans using an integer, and so working with Waters data with duplicate scan numbers with different functions is problematic, as least in setting up the internal references to individual scans. There are several options for compensating for this, but I don't know enough about waters functions/scans to choose one that will reasonably represent the data file. I can see that your data has 4 functions, where functions 1 and 4 are MS1, and functions 2 and 3 are MS2. Also, I noticed that it is IMS (or TW-IMS) data; you are venturing into uncharted territory with MSPathFinder...

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PNNL-Comp-Mass-Spec/Informed-Proteomics/issues/8#issuecomment-342273714, or mute the thread https://github.com/notifications/unsubscribe-auth/AErvpwQz5gbjyF8BCAIXgC8AkGHByajNks5sz2nygaJpZM4QQfQ2 .