Question

Application of Deseq2 to mass spec data

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maduanduan8 • 0

@maduanduan8-13146

Last seen 7.8 years ago

It looks like DESeq2 has been used efficaciously for MS data in published papers (https://www.ncbi.nlm.nih.gov/pubmed/?term=26193490). However, that is for unlabeled MS data, in which the only information is the spectral count. For labeled MS data, it does not appear DESeq2 is being used.

Thus we want to double check with you that Deseq2 is appropriate for labeled mass spectrometry counts. We will also greatly appreciated it if you could send us some publications in this area.

Thank you so much!

deseq2 • 5.2k views

ADD COMMENT • link updated 7.8 years ago by Laurent Gatto 1.6k • written 7.8 years ago by maduanduan8 • 0

score 3 · Answer 1 · 2017-06-04

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Laurent Gatto 1.6k

@laurent-gatto-5645

Last seen 29 days ago

Belgium

The only type of MS-based quantitation that is amenable to DESeq2 (or similar approaches) is spectral counting. Other approaches, whether labelled of unlabelled, are continuous data; I would also recommend limma for their analysis.

ADD COMMENT • link 7.8 years ago Laurent Gatto 1.6k

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What's your take on normalization/computing offsets? I usually take the super naive approach of assuming that the assumptions underlying the methods used in DESeq2 or edgeR are +/- applicable to spectral count data, but given the unfortunate level of missingness (here I am talking about data that appear to be missing at random), I have never quite convinced myself that this is really a smart thing to do.

ADD REPLY • link 7.8 years ago James W. MacDonald 68k

score 2 · Answer 2 · 2017-05-30

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

I think the key considerations for use of DESeq2 are: (1) are the data roughly count scale, and so the negative binomial variance modeling is useful, (2) can you assign observations to rows with some certainty (or if not extra modeling is needed to deal with this uncertainty but this is not part of DESeq2 right now)

ADD COMMENT • link 7.8 years ago Michael Love 43k

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I asked Laurent Gatto, and he said It probably only makes sense for spectral count data (other data not counts).

ADD REPLY • link 7.8 years ago Michael Love 43k

score 2 · Answer 3 · 2017-06-02

I don't think I know all the different varieties of MS data, but for many quantitative MS data types, it is appropriate to treat them as continuous measurements on which you can use ordinary statistical models and tests, possibly with empirical Bayes moderation (limma) and/or suitable transformation (e.g. https://www.ncbi.nlm.nih.gov/pubmed/20382981)