Issue 1008: include more .D metadata in Skyline replicates

Assigned To:Matt Chambers
Opened:2024-02-07 09:41 by Brian Pratt
Changed:2024-03-08 09:29 by Brendan MacLean
2024-02-07 09:41 Brian Pratt
Title»include more .D metadata in Skyline replicates
Assigned To»Brendan MacLean
Notify»cian monnin
per and related email exchange of Feb 6 2024 between BrianP and MattC on the dev group:

Chambers, Matthew
7:55 AM (1 hour ago)
to me, skyline-dev

Yes, it's on the pwiz side (HandlerDevices in MassHunterData.cpp). The sample name would be set with an MS_sample_name CVParam in a Sample object in the MSData::samplePtrs vector. Reader_Thermo already sets it and MsDataFileImpl has a way to access it (GetSampleId).

On 2/6/2024 5:34 PM, Brian Pratt wrote:
Nice. That's on the pwiz side, yes? Where would this kind of extra info fit in the mzML schema?

On Tue, Feb 6, 2024 at 2:05 PM Chambers, Matthew <> wrote:
No, but we do already parse the Devices.xml file to get the instrument serial number. Parsing that sample_info.xml file looks quite trivial.

On 2/6/2024 4:56 PM, Brian Pratt wrote:
@Matt - is that kind of info available in the Agilent API? If so we could add it as a replicate annotation in Skyline.

---------- Forwarded message ---------
From: Skyline Support <>
Date: Mon, Feb 5, 2024 at 1:17 PM
Subject: When importing Agilent .D files is there a way to read the Sample Group information?
To: <>

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cian monnin (DailyRequests) created a new request    2024-02-05 13:17
Hello Skyline Team!

When making a worklist on Agilent's Data Acquisition software there is a Sample Group column. Is there a way to import or populate a column with this information in Skyline? It's stored in the the sample_info.xml as

    <DisplayName>Sample Group</DisplayName>
Specifically the <Value>20x_MEF_NPRL2</Value> is of interest for us.


2024-03-08 09:29 Brendan MacLean
Assigned ToBrendan MacLean»Matt Chambers
Matt, I think you would be the person to do this, since you added the sample name value for The Broad from Thermo raw files.