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

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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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Hugo López-Fernández, PhD
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