#4 apply to all

[geert goeminne]

Hi,would it be possible to, for example when uploading 100 compounds, select all of them at once and then apply the intensity cut off to all of them at once? Now you need to do one by one, would be nice to enable this for all at once?
Second question, when using the plugin PQILIMA.dll and changing the headers, this is a fixed change, is there any way i can choose myself which header input is removed and/or modified/replaced?

Thanks a lot,

Cheers, Geert

[clochardM33]

Part 1 - Apply intensity to all.
This would probably be a plugin function. Will look into it.

Part 2 - Changeing params.
The plugin system does support a simplistic parameter file mechanism. In PQLIMA it isn't implemented as it was intentionally a fixed list of adjustments.
However this might not be as useful as it sounds.
It isn't easy to pass logic in a parameter file (such as for ABC do DEF conditional on GHI), but it is easy to pass 1:1 mapping (such as if ABC exists add "Hello world").
Give me some examples of what you are thinking off and we can see where it goes.

[geert goeminne]

Hi,

part 1: ok, that sounds great, since we are mainly doing untargeted metabolomics, we have to deal with often hundreds or even a couple of thousand MSMS spectra that we upload in MSFinder for potential unknown annotation. The header that MSFinder request is fixed and needs at least these 4 inputs:

PRECURSORMZ:
PRECURSORTYPE:
Ionmode:
SPECTRUMTYPE:

Progenesis QI does not export these as mentioned before, but that is the case when you only use [M-H]- of [M+H]+ as adducts for compound detection. When you use [M+2H]+ for example, and it found a double charged compound, then it will calculate what is the [M+H]+ as well, and it will export it in the msp (this means the header line "Charge: 1-" is not there anymore for that compound. But the header input will be for example Precursor_type: and not PRECURSORTYPE: , so MSFinder will not read this header as it needs exactly PRECURSORTYPE: An example file is in attachment, called Multiple charged from PQi. This is a bit annoying because it also does that for Formic Acid ([M+FA-H]-) for example and sodium adducts. I have requested to Nonlinear/Waters already to adjust their export to something more uniform and consistent, but since two years now there are issues between Nonlinear and Waters and no development or improvements are currently done when sending requests.. This is why i was looking for something like MSP Librarian.

So in the example file, Precursor_type should be changed to PRECURSORTYPE, and for that compound the Ionmode should still be added as well, cause that is not added since the PQILIMA plugin did not detect "Charge:"

An example of that is found in the PQILIMA second file i have attached, look for compound unknown (13.40_1087.5097n) for example.

Part 2: I honestly do not understand what you mean (i'm not a programmer at all, I have no basic skills in that, would love to but don't have the time)

Let me know what you think, but the easiest way would be that Progenesis exports in a more uniform format I would think....

Cheers, Geert

[clochardM33]

At the moment the intensity cut off is an integer percentage of the largest intensity in the data.
For example 1%, or 2%, but not 1.5%.
This stays.

I can make a plugin that is a little bit different from the Editor page in that it separates the normalise and the intensity cut off. At the moment they are done as a pair or not at all.
There would be a parameter file for:

1. Percentage intensity of largest peak
2. Use Intensity cut off
3. Normalise to "this intensity"
4. Use normalise

Is this the sort of thing you were thinking of for this ticket?

[geert goeminne]

hmm I think we are misunderstanding each other. My question was, if you upload an msp file containing 20 entries (20 different compounds), you can edit them one by one (meaning removing noise peaks in the spectrum), but it would be nice if you select them all 20 at once and apply the "spectrum clean up"for all seceted compounds, indeed as a percentage of the largest peak present in each spectrum. An integer percentage is fine.

[clochardM33]

It's ok. We are talking about the same thing as each other.
Plugins are applied to all entries either when they are read in (Read Plugins) or when they are Saved (write plugins).
You want a Write plugin that applies the spectrum clean up to every entry in one click.
Note: The one thing that cannot be done is applying plugins to a selective list of the entries.

[clochardM33]

There is now a plugin for this.
It is at the \Other Plugins page.
There is also an update for the miing zero intensities.
That is at \Updates

The wiki page for how to use is here
[Normalise Intensity Plugin]

Can you copy the second part of the info above to a new ticket please then I can close this one.
If there is anything more on this plugin just start a new Ticket.

[clochardM33]

This is picked up in Ticket 7