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kevinkovalchik / RawQuant

RawQuant is a Python package for extracting scan meta data and quantification values from Thermo .raw files.
MIT License
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MS1 scan number off by one in SPS MS3 QuantData report #15

Open pwilmart opened 6 years ago

pwilmart commented 6 years ago

Hi, I am trying out RawQuant and was checking the mapping of MS3 to MS2 scan numbers for some SPS MS3 data. That looks good. However, the MS1 scan numbers seemed to be off by one scan number (one less). Cheers, Phil

kevinkovalchik commented 6 years ago

Hi Phil!

I have a few questions:

  1. What instrument is the data from (e.g. fusion, exactive, etc)?
  2. Are you using RawQuant from PyPi or the latest master from GitHub?
  3. Is it a standard sps-ms3 experiment or are you doing something with unusual MS1 scans like boxcar?
pwilmart commented 6 years ago

Hi Kevin, An early Fusion with latest Thermo control software.

From PyPi (following the installation instructions (https://github.com/kevinkovalchik/RawQuant/blob/master/docs/RawQuant_Instructions_ver-May2018.md)

Standard SPS-MS3 Cheers, Phil

kevinkovalchik commented 6 years ago

Alright, thanks. If I get a chance I'll look into it this weekend. Otherwise might be until Monday or Tuesday.

pwilmart commented 6 years ago

Hi Kevin, No worries and no rush. The MS2 and MS3 scan numbers look correct and those are the important ones for the TMT stuff. I think the MS1 retention times might be associated with the incorrect scan numbers. I think the times were not matching what was in the file from MSConvert (when I was looking yesterday). I do not have QualBrowser or Freestyle installed on my home computer so I can’t directly open the RAW file and double check things. Thanks for looking into this. Cheers, Phil

On Aug 26, 2018, at 9:52 AM, kevinkovalchik notifications@github.com wrote:

Alright, thanks. If I get a chance I'll look into it this weekend. Otherwise might be until Monday or Tuesday.

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pwilmart commented 6 years ago

Hi Kevin, I also have some questions about columns in the QuantData table. These are for the blocks of 10 TMT channels: _mass - the m/z of the chosen reporter ion peak _ppm - the delta mass between chosen peak and theoretical position (in PPM) _intensity - the peak height (or the centroid intensity value) of the chosen reporter ion peak _res - ??? _bl - ??? _noise - the FT noise level for the respective reporter ion region

Are _res and _bl (maybe) resolution and baseline? What exactly are _bl numbers? Are these negative because Thermo subtracts the transient background from the signal (or something like that)? The JPR paper compares RawQuant values to PD values for signal-to-noise ratios. Are those computed from the intensities and noise columns? I did not see an option flag in the help information related to S/N ratios. Thanks! Cheers, Phil

kevinkovalchik commented 5 years ago

Hi Phil,

Sorry for the delay. I am not seeing the same issue with the MS1 scan numbers on RawQuant. This might be an issue with the last PyPI release, so I'll check that out and see about putting up a new release on PyPI. You could try installing from the master branch to see if this changes things. If you think RawQuant is something you would use regularly or occasionally, you might want to check out our new project RawTools. It is essentially a new version of RawQuant written in C#, which means it is a standalone program (aside from meeting the .NET requirements). It will get most of our attention from now on.

For your questions, yes _res is the resolution of the respective peak. I believe you are correct that the _bl numbers are negative because they are the values used to subtract the background. I haven't used these for much myself, but we thought they might be of interest.

kevinkovalchik commented 5 years ago

Oh, and yes S/N was calculated directly from the intensity and noise columns.

pwilmart commented 5 years ago

Hi Kevin, I will checkout RawTools. Thanks for the information on that. Cheers, Phil

kevinkovalchik commented 5 years ago

Sure. I hope it turns out to be useful for you.

Take care, Kevin

On Thu, Oct 4, 2018, 5:52 PM Phillip Wilmarth notifications@github.com wrote:

Hi Kevin, I will checkout RawTools. Thanks for the information on that. Cheers, Phil

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