Re: [Psidev-qc-dev] Quality control in Mass-Up (and other topics)

[David T. <dt...@su...>]

I really appreciate it, sir!

Our meeting will take place from April 18-20th.  If we can discuss it
during the 19th, that would be ideal!

I have included your image in the update I will be providing at the
start of the meeting (see attached).

Merci,
Dave

On 4/11/2018 11:40 AM, Hugo López Fernández wrote:
> Hi David,
>
> sure, I would be pleased to provide such draft. Please, let me know
> the deadline for sending you the document. I will have a meeting
> tomorrow or the day after tomorrow with my Mass-Up collaborators to
> address this.
>
> Regards,
>
>     Hugo.
>
> El 11/04/18 a las 09:41, David Tabb escribió:
>> Hi, Hugo.
>>
>> Would you be willing to assemble a draft qcML document that might be
>> created by your Mass-Up software?  We will be looking at such examples
>> at our annual HUPO-PSI meeting in a week.  I am providing a pointer to a
>> draft qcML example of the quality metrics that are produced within the
>> QuaMeter "IDFree" mode.
>> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml
>>
>>
>> Thanks,
>> Dave
>>
>> On 1/20/2017 1:31 PM, Hugo López Fernández wrote:
>>> Hello David,
>>>
>>> I am Hugo, we met last week in Semmering. I hope this email finds you
>>> well and that you had a good trip to back home.
>>>
>>> As we talked in the EuBIC, I am writing you to let you know more about
>>> the quality control analysis that we have included in Mass-Up
>>> (http://sing-group.org/mass-up/). This quality control is intended to
>>> work with peak lists. We would like to incorporate quality control for
>>> raw data, specially to detect batch effects as I also commented you.
>>>
>>> Basically, the quality control (which is explained with most details
>>> in the paper http://doi.org/10.1186/s12859-015-0752-4) can be done at
>>> two levels: at the replicates leve and at the samples level, which
>>> includes additional information from the intra-sample m/z matching
>>> process and consensus spectrum creation (this is because our
>>> collaborators usually want to reduce replicates spectra to a unique
>>> sample "consensus" spectrum). You can find attached the quality
>>> control image included in the paper.
>>>
>>> At the replicates level, the user can check basic information about
>>> each individual spectrum (i.e. peak count, m/z range, intensity
>>> ranges, etc.) and compare all spectra in the dataset. At the samples
>>> level, the user can check the performance of the intra-sample peak
>>> matching process, by comparing the percentages of presence (POP)
>>> counts (i.e.: the counts of peaks that are present in, for example,
>>> 60%, 80% or 100% of replicates) and the POPs of each sample.
>>>
>>> In spite of being a very simple quality control it allowed us to
>>> detect some problems with datasets and we encourage our collaborators
>>> to have a quick look at this quality control metrics before any other
>>> analysis. Unfortunately they usually don't but we must encourage good
>>> practices, which is the reason why I am developing this other software
>>> (http://www.sing-group.org/s2p/), also presented in other poster at
>>> the EuBIC. Basically it is a software to manage, process and integrate
>>> different data sources (Mascot identifications, MALDI plates, 2D-gel
>>> spots). It probably will not revolutionize bioinformatics but it is
>>> allowing the research group to process data efficiently and in a
>>> reproducible way, a totally different scenario than wen I came here
>>> six months ago.
>>>
>>> As I mentioned previously we also would like to include quality
>>> control metrics for MALDI-TOF raw data, with special focus in batch
>>> effect detection (which seems to a common problem here). Regarding
>>> batch effect, I would like to apply this statistic
>>> (http://dx.doi.org/10.1093/bioinformatics/btt480) based on guided
>>> principal component analysis to detect batch effects in MALDI-TOF data
>>> (some people applied it to LC-MS metabolomic data
>>> [http://dx.doi.org/10.1016/j.talanta.2014.07.031]). I would like to
>>> develop this work this year if I get public MALDI-TOF datasets where
>>> batch effect presence has been publicly reported (I found a few
>>> reported but I could not get the data to analyze it yet).
>>>
>>> I will be happy to answer any question you may have or to receive any
>>> feedback from you. Looking forward to see you again, in other
>>> conference or wherever.
>>>
>>> Best regards,
>>>
>>>     Hugo.
>>>
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