Error parsing Precursor Ion Scan files

[alliemiskulin]

Hello, I am attempting to parse .RAW files for a precursor ion scan method collected on a TSQ Fortis instrument, and am gettting the following error for every scan:

ERROR Scan #27 cannot be processed because of the following exception: Specified argument was out of the range of valid values.
Parameter name: Unknown msLevel: -1
at ThermoRawFileParser.Writer.MzMlSpectrumWriter.ConstructMSSpectrum (System.Int32 scanNumber) [0x0060a] in :0
at ThermoRawFileParser.Writer.MzMlSpectrumWriter.Write (ThermoFisher.CommonCore.Data.Interfaces.IRawDataPlus rawFile, System.Int32 firstScanNumber, System.Int32 lastScanNumber) [0x00ce3] in :0

Other scan types collected on the same instrument do not yield this error.

[caetera]

Hi @alliemiskulin ,

Thank you for reporting this. Is it possible for you to share an example of such file?

[alliemiskulin]

Hi @caetera, thank you for your quick response. Here is an example file: https://drive.google.com/file/d/1Pq32fvWNXT9tyiK-1uu6IxLItjiuDGCf/view?usp=sharing

[caetera]

Thank you for sharing the file. Precursor scans (as well as neutral loss and neutral gain ones) are not supported. There is no fast fix for this - I will schedule this feature for the future release.

[alliemiskulin]

Thank you for looking into this

[caetera]

Hi @alliemiskulin,

I have implemented the precursor-ion scans in the latest draft release - https://github.com/CompOmics/ThermoRawFileParser/releases/tag/v.1.5.0-alpha.2

Since I don't have a lot of experience with triple quads, I am not fully certain that I the information about the precursor in the right place. The output now is similar to targeted MS2 scan - there is no parent scan and, thus, charge and intensity of the precursor is unknown, but selected precursor, isolation window, and fragmentation are reported. Could you, please, confirm that the output make sense.

As a side note, do you happen to have some neutral-loss and/or neutral-gain files that you can share with us, then I can check if these scan types are processed correctly.

[alliemiskulin]

Hello, My apologies for the delayed reply, I have been on vacation the past 2 weeks. I will test this out and confirm it is working sometime this week Thanks!

…

On Tue, Aug 12, 2025 at 7:59 AM Vladimir Gorshkov ***@***.***> wrote: *caetera* left a comment (CompOmics/ThermoRawFileParser#197) <#197 (comment)> Hi @alliemiskulin <https://github.com/alliemiskulin>, I have implemented the precursor-ion scans in the latest draft release - https://github.com/CompOmics/ThermoRawFileParser/releases/tag/v.1.5.0-alpha.2 Since I don't have a lot of experience with triple quads, I am not fully certain that I the information about the precursor in the right place. The output now is similar to targeted MS2 scan - there is no parent scan and, thus, charge and intensity of the precursor is unknown, but selected precursor, isolation window, and fragmentation are reported. Could you, please, confirm that the output make sense. As a side note, do you happen to have some neutral-loss and/or neutral-gain files that you can share with us, then I can check if these scan types are processed correctly. — Reply to this email directly, view it on GitHub <#197 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AZDR2AUUSVR4Q7AG3CVVGOL3NH6LLAVCNFSM6AAAAACCJY3MXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCNZZG4YTSNRTGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[alliemiskulin]

Hi @caetera ,

I am still working on confirming that the information is in the right place.

In the meantime, here is a file that contains NL data: https://drive.google.com/file/d/1elhmqYjGnsI94w_OHWFiq64B5L2t4ALu/view?usp=drive_link
This file has combined PIS and NL data, where the NL data is collected from 1.1-2.0 min of the scan

Thanks for your work on this issue!

[alliemiskulin]

Hi @caetera,

Thank you for implementing the precursor ion scan in the draft release. I have now confirmed that the precursor info is in the right place.

If you require any additional info, please let me know.

Thanks!