MRM peak integration

[cobbolds]

Hi, I was trying to use an SRM library to extract some mzXML files I acquired off an Eclipse (Thermo), targeted MS2. The idea was to use one of the MS2 ions for quantification but when I use an SRM library (for example, a single MS1 species, fragmented and one MS2 ion defined), the MS2 target ion looks incomplete (scans missing) and low intensity compared to visualising the same MS2 ion extracted via Thermo Freestyle.

I think it is likely that I am doing something wrong, but I am not sure how best to go about doing this successfully. I am converting the .raw files with MSConvert into mzXML using the vendor peak-picking for MS1.

Thanks in advance for any suggestions.

Simon

[PMSeitzer]

Thanks @cobbolds for your interest in maven.
In terms of SRM data, in recent years MAVEN has been optimized to work with Sciex 7500 data. It's possible that there are some differences between the instrument you're using and the 7500 which are causing the problem.
If you're using SRM data, You could try to view your data in the Widgets -> SRM List or Widgets -> SRM Transition List from the program's main drop-down menu.

I'm not sure why the EIC widget is showing a truncated form - perhaps you could try opening your file in a newer version of MAVEN? The latest version is 2.10.21
https://github.com/eugenemel/maven/releases/tag/2.10.21
In the program options, under Instrumentation, you can set the Q1 and Q3 tolerance values - if these are set at 0 there could be some floating point rounding errors which could be excluding some of the intensity you're seeing. You can access this window by clicking the Options button from the main window toolbar.

[PMSeitzer]

@cobbolds Just wanted to check in and see if you had a chance to revisit this issue. If you would like, you can send me your files by sending them to maven2software [at] gmail [dot] com and I'll be happy to see if I can reproduce your issue.

[cobbolds]

Hi Phillip, apologies for the non-response. I tried both of your suggestions (latest version and widening the tolerance values) but I still get the same truncated peak for the PRM of interest.

The file is 120 Mb, I have uploaded it to a Dropbox folder and allowed access to the suggested email. Thanks in advance.

[PMSeitzer]

@cobbolds Thanks, I received your file - will take a look!

[cobbolds]

Hi Phillip, I just uploaded the file into the Google Drive folder. Thanks again, Simon

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____________________________________________ Simon Cobbold PhD Research Fellow Komander Lab Ubiquitin Signalling Division WEHI 1G Royal Parade, Parkville 3052 VIC, Australia

________________________________ From: Phillip Seitzer ***@***.***> Sent: Friday, 17 January 2025 4:57 AM To: eugenemel/maven ***@***.***> Cc: Simon Cobbold ***@***.***>; Mention ***@***.***> Subject: Re: [eugenemel/maven] MRM peak integration (Issue #764) @cobbolds<https://github.com/cobbolds> Thanks, I received your file - will take a look! — Reply to this email directly, view it on GitHub<#764 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AQUYEHIUV7DDBEQQYOTVTML2K7XIHAVCNFSM6AAAAABTRG6WESVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKOJWGM3DGOJVG4>. You are receiving this because you were mentioned.Message ID: ***@***.***>