Skip to content

Commit

Permalink
Update 09-metabolomics.md
Browse files Browse the repository at this point in the history
corregí dos figuras, las listas y un titulo
  • Loading branch information
andrespan authored Aug 21, 2024
1 parent 29d2273 commit a6bbb10
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions _episodes/09-metabolomics.md
Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ In addition, there is information relevant to the analysis, such as the names of

At last, there is a file named MZMine_FBMN_batch.xml that collects all the information necessary for the analysis using MZMine

** Analysis using MZMine
## Analysis using MZMine

Load batch file

Expand Down Expand Up @@ -180,7 +180,7 @@ The software will display the Total Ion Chromatogram (TIC) from both samples. In
We can select a section of the chromatogram to inspect the differences of the metabolomic profiles of these samples

<a href="../fig/chromatogram_04.jpg">
<img src="../figs/chromatogram_04.jpg" alt="Chromatogram" width="800"/>
<img src="../fig/chromatogram_04.jpg" alt="Chromatogram" width="800"/>
</a>

We can observe that several spectra are produced exclusively by strain H-KF8 in ISP2-ASW
Expand Down Expand Up @@ -316,7 +316,7 @@ Click on that folder. Then in the "File Drag and Drop", drag and drop the follow
Return to the "Select Input Files" after uploading your files. You should be able to see the three uploaded files in your directory

<a href="../fig/FBMN_05.jpg">
<img src="../figs/FBMN_05.jpg" alt="FBMN" width="800" />
<img src="../fig/FBMN_05.jpg" alt="FBMN" width="800" />
</a>

We are going to select the "GM_workshop_Featurelist_filtered.mgf" file as "MS2 file in MGF format"
Expand Down Expand Up @@ -346,9 +346,9 @@ Click on finish selection after checking everything is ok.

After selecting the files, we need to adjust the parameters for our network
Since our data was collected using a high-resolution LC-MS/MS, we could adjust the
-"Precursor Ion Mass Tolerance" to 0.02 Da
- "Precursor Ion Mass Tolerance" to 0.02 Da
This value affects the clustering of nearly identical MS/MS spectra through MS-Cluster.
-"Fragment Ion Mass Tolerance" to 0.02 Da
- "Fragment Ion Mass Tolerance" to 0.02 Da
Sets the allowable deviation in m/z values for fragment ions when clustering MS/MS spectra

<a href="../fig/FBMN_10.jpg">
Expand All @@ -357,9 +357,9 @@ Since our data was collected using a high-resolution LC-MS/MS, we could adjust t

Then we need to select our thresholds to create the molecular network

-"min pair cos" to 0.7
- "min pair cos" to 0.7
The minimum cosine score required between a pair of consensus MS/MS spectra for an edge to be created in the molecular network.
-"Minimum matched fragment ions" to 6
- "Minimum matched fragment ions" to 6
Specify the minimum number of common fragment ions that two consensus MS/MS spectra must share to be connected by an edge in the molecular network.

<a href="../fig/FBMN_11.jpg">
Expand Down

0 comments on commit a6bbb10

Please sign in to comment.