How to collect GC-MS Spectra for GC-AutoFit

How to collect GC-MS Spectra for GC-AutoFit (GC-MS Sample Preparation Protocols)

How to use GC-AutoFit (General Instruction)

General Instruction

Required Spectrum Files for using GC-AutoFit

Three types of input files are required:

Preparing Alkane Standards

The retention times of alkane standard peaks are used for calculating the retention indices of each sample's peaks. The required range of alkane standards is from C10 up to at least C36, as shown below.

Alkane profiled bbe4845e999242f6078b4eef3e23f1d5c672883812d92da3d7c06bbd782fb828

Converting File Formats (.CDF or .mzXML)

GC-AutoFit expects a file in .CDF or .mzXML format as input. If you are using Agilent's .D file format, you'll need to convert your input to .CDF or .mzXML format.

Conversion Software:

Choosing a Library and Internal Standard

You can choose to use one of internal libraries or upload your own library. You must select or submit an internal standard for quantification.

1) Select Biofluid type to use an Internal Library or Select the 'Upload Your Library' to use your own library.

Select biofluid 4d1581489de32bcdf5db6a90de122a3f7357b36fb0a905075094c86d7e1a3e4a


Upload userlib 0a55450629ff2078bd6c4d40aff135fab0ffde6856314ccb8f45185ce1441cbd

2) When you select a Biofluid type (e.g. "Serum") for the internal library, you can see the list of metabolites in that library by clicking the blue icon on the right side of Biofluid. You can choose all the metabolites or select a subset of them.

Listofcomps c5b8c020357b9d546995c1255dc8626d2bd0f51ed2ddbe2357702709dd5c310d

3) To quantify concentrations, you must specify the compound name of the internal standard. You can select one from the list or enter your own in the textbox by the choice 'Other'.

Select istd db9525fc08c78a4df26751393bd2fe85213daefabd0eeae0b4061e3afbdd8182

Uploading Spectrum Files

There are two ways to upload files. The first is to upload the Alkane Standards, Blank, and Sample files individually.

Upload separate 49774b74b022d5a8091c35cb802a72005e54b79e8f869a4ca20f365addc0868d

The second way is to upload a single zip file that includes all three types of spectrum files, named accordingly.

Upload zip 133f659366404cac8df67c8e79d73d12137ace34546e8b7ab5162294e89a2dc4

Checking Spectrum (Alkane Standard and Sample Spectra)

Before profiling, check over the Alkane Standad, Blank and Sample spectra, including any quality control spectra you may have. If any of the Alkane Standard values are wrong, click on the value and correct it.

Check spectrum 53b6b11b1a16fdc4c1cd51f773b783fb00b0d4f014557ade3ee4145d62ae2b61

Perform Profiling

If there are no issues with the spectra, start profiling by clicking the Profile button.

Profile button 0d2fbf75aa3b7e8c9d6e4e5fb21124b754077c72047fadf44a9974e9f114d845

You will be taken to the Profiling page where the status of your spectra will be shown.

Profiling status d443cd484cff0898a571723dd6c090ad9647da0f733213c824ddf1b1f144eb0c

Getting Results for each Sample and the Final Concentration Table

Once a sample has been profiled you can click on it and go to the Results tab to view the spectrum with assigned metabolites. The Download CSV

Results page:

Result all ad8ce3e62e3067f17df6a3da06426afd2d778d510925ec7dc7f0a3d3af9472fd

Porfiled table:

Result table 72a22fdeaab2452d265a7ea802c2a930a974ad06bac8100bed39d4691d3f3de2

Spectrum plot (identified compound names, can be zoomed in/out):

Result spectrum b7a60f8566a92a4db772f85b5068d2477d8f88543a41310844e3f7fe40438931

Merged concentration table (download CSV file by click the 'Download Results'):

Once all of the samples have been profiled, you can click the Download Results link in the Profiling tab to get a concentration table for all the samples.

Result concentration fdaf1c6b91a49f5f30e6337b7d56122661bda9fb2d0f039ad71f0f4f304d3d5b