mz values less than 1

[zsgit01]

Hi,

I converted the file 20241224_AST0_NEO4_JVO_IO15_HeK_100ng_Astral_all_50SPD_04.raw from dataset PXD067317 using default options. I noticed that in one scan there are several peaks with m/z values less than 1, which cause problems during the DIA-NN search.

TITLE=20241224_AST0_NEO4_JVO_IO15_HeK_100ng_Astral_all_50SPD_04.149368.149368.
RTINSECONDS=1203.844893
PEPMASS=698.56738 23592311.125
1.934887768e-19 160.4001312256
3.934978293e-14 60559778088461496224462.0
2.617579764e-12 0.0
2.086415624e-10 62050514601117400648822.0
2.69461764e-09 3173708329426913848488868026480.0
1.097754375e-05 0.0000000026

These peaks do not appear in the mzML file generated using msconvert. Could you please take a look to see if this might be an issue with the conversion?

-Zhi

[caetera]

Hi @zsgit01,

Thank you for using ThermoRawFileParser. Unfortunately, I could not reproduce the error with the latest version of TRFP.

Could you, please, include the following information to help in reproducing the error?

• OS
• Version of ThermoRawFileParser
• Build type (Docker/Standalone/Framework)
• Dotnet/mono version, if applicable
• The command that you use for the conversion
• Any "common" checksum for the input file (i.e., MD5, SHA1, SHA256, etc); SHA1 is computed by TRFP and written in the header of mzML file

[zsgit01]

OS: Ubuntu Linux (64-bit) with kernel 6.8.0-45.
Version of ThermoRawFileParser: 2.0.0-dev
Build type (Docker/Standalone/Framework): ThermoRawFileParser-v.2.0.0-dev-linux.zip
Dotnet/mono version: mono JIT compiler version 6.8.0.105

The command that you use for the conversion:
ThermoRawFileParser -i="20241224_AST0_NEO4_JVO_IO15_HeK_100ng_Astral_all_50SPD_04.raw" -f=2 -o="./" -m=1

Any "common" checksum for the input file (i.e., MD5, SHA1, SHA256, etc); SHA1 is computed by TRFP and written in the header of mzML file
name="SHA-1" value="905e255a05987a95d43cc91e96da60d1f38ba265"

[caetera]

I can see that the file I have downloaded from PRIDE for testing has a different SHA1 hash

> sha1sum 20241224_AST0_NEO4_JVO_IO15_HeK_100ng_Astral_all_50SPD_04.raw
b1586f3f6da67c01747d1c9cfffac373b4d21cb2  20241224_AST0_NEO4_JVO_IO15_HeK_100ng_Astral_all_50SPD_04.raw

Unfortunately, this dataset does not contain the "reference" checksum file. Most likely, the error you are facing is due to data corruption during transfer. Could you, please, try to download the file again.

[zsgit01]

Thanks for checking. You are right—I downloaded the file again, and the problem was resolved.