Read out scan header metadata for TIC and BPC?

[WeiqiangChen]

Hi,

is there a parameter to read out each scan metadata, such as Scan number, Base peak intensity, total ion current intensity, Scan node, Ion injection time, and store it in Json or parquet?

I could sum up intensity of each peak from each spectrum to get TIC, and max(intensity) to get BPC, but it is too slow.

Thank you !

Best regards,
WeiQiang

[caetera]

Hi @WeiqiangChen ,

Unfortunately, this kind of metadata is not implemented in ThermoRawFileParser.

There is another tool - https://bitbucket.org/caetera/scanheadsman/src/master/ - that can export the data you need in a CSV format.
You can run it with -d header (default) and rely on BasePeakIntensity as provided in the scan header, or with -d small, then the output will include maxInt column, which is the intensity of the largest centroid in the corresponding scan.

This metadata format can be included in TRFP in the future.