LC-Inspector can be used to analyze mass spectrometry data (MS Only), chromatography data (LC/GC Only), or both at the same time (LC/GC-MS).

Jump to section:
LC/GC-MS
MS Only
LC Only

As not everyone makes use of the chromatography data when running LC-MS or GC-MS, and similarly not everyone runs their chromatography coupled to an MS, LC-Inspector was designed with this flexibility in mind.

The modes can be changed with a combo box on the Upload tab.

LC/GC-MS

LC/GC-MS is the default mode in which LC-Inspector will launch. In this mode, the input requires chromatography data in text format (as either TXT or CSV files). The expected format is columns of numbers, where the first column is the retention time (RT) and the last column is the intensity value (e.g., absorbance), with optional columns in between (i.e., detector step size, additional wavelengths, etc.). If a header is detected in the file, it will be automatically skipped until columns of numbers are detected.

Expected format (example ThermoScientific Chromeleon output):

Channel	UV_VIS_1                                |
                                                |
Injection Information:                          |
Data Vault	ChromeleonLocal                 |
Sequence	example-sequence-name           |  This part is skipped
Name            example-sample-name             |
...                                             |
Chromatogram Data:                              |
Time (min)	Step (s)	Value (mAU).    |
0.008467	n.a.	0.000000
0.025100	0.998	0.000040
0.041767	1	0.000280
0.058433	1	0.000860
0.075100	1	0.001680
0.091767	1	0.002450
0.108433	1	0.003100
...

Subsequently, the values get read into a pandas DataFrame and baseline correction is performed using the SNIP algorithm.

[!IMPORTANT]
The MS input requires mzML files (support for mzXML, TXT, HDF5 and other open formats is planned) which need to be the same name as the corresponding chromatography files if they are supposed to be treated as the same experiment.

The last input is the desired compounds to be traced -- this includes any m/z values, at any decimal precision. The default precision is 0.0001 which corresponds to resolving power of about 1'000'000 (e.g., FT-ICR). The precision is adjusted automatically based on the input data.

The output consists of 4 panels:

• the original and baseline corrected chromatograms
• the interactive mass spectrum, changes when clicking on the chromatogram (or using left-right arrow keys to go scan by scan)
• the annotated chromatogram: the highest intensity of the traced compounds during run is assigned to the chromatographic peak corresponding by retention time
• the extracted ion chromatograms of the traced compounds (MS intensity over retention time)

Example:

MS Only

The MS Only mode requires mzML files as input and simplifies the analysis to only tracing ions within the mass spectometry data. The chromatogram is then substituted by the Total Ion Current (TIC).

[!TIP] If the file includes ion mobility scans, they are going to be treated as chromatography files instead of the TIC.

Example:

LC Only

TODO