LCMS tutorial leads to error

Following tutorial attached. Tried to setup data as per tutorial 2nd attached. Got error 3d attached.

What am I doing wrong?


Hi @robk,
your dataset is already a collection; you can jump to the next step.


Thank you Thank you. I was extremely frustrated and really wish that I could have found a video of someone processing LCMS. Each tutorial resulted in my missing some important item or the tutorial was not correct.

I am new to MS processing.

I have 10 .mzML files, 5 male and 5 female of about 150Mb each.

I want to compare the metabolites of both sexes to “known” metabolites in mice.

Most importantly, I’m looking for sex specific metabolites (SSM), meaning metabolites that are only in one sex. I understand that this is a problem for processing because stats will not handle empty cells of data, thus a low value is automatically put into cells of 0 value, thus the end results have no SSM.

I must be gone for 10 hours from the time of this reply for family responsibilities.

I realize that I had three datasets that I was working on sacurine, mg11-15 and fg21-25. Which one are you speaking about? Learning how to do any would greatly help with all.

Thanks again,

Rob Kleps


I got a break to write this reply.

I’m following a tutorial see 5 attached. When I looked for a tool xcms-Findchrome… in the tool box “xcms” found nothing. I tried “find” and found nothing.

I don’t know where I can find this xcms-Findchrome … process.

If I just use the tool box, I don’t know the names of the tools I should use. If you are familiar with LCMS processing can you give me the toolbox names that I should use?
#4, etc
#? tool for finding differences between these males and the 5 females.


I’m asking what is the next step in processing and how do I get it. 20210315:20:45

What are the names of steps used in LCMS data?
Is there a hand book available for LCMS?


Hi @robk,
it seems that you are using the explanatory slides, instead of the training: please have a look at this links:

Let me know if you have any doubt after reviewing the tutorials.


The last one LCMS-preprocessing is what I was following and trying to use the “tools” list".

I would greatly appreciate a slow video of where and how to use tools to process my other two 5 file datasets.

thank you,


I found the attached URL, but I don’t know what I can do with the tools and I don’t know how to get and use them.

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