SpectronauttoMSstatsFormat()

[Tobias Kockmann]

Hi MSstats maintainers,

I discovered the following function in the MSstats 3.6 vignette:

SpectronauttoMSstatsFormat {MSstats}

R Documentation

Generate MSstats required input format for Spectronaut output

Description

Convert Spectronaut output into the required input format for MSstats.

Usage

SpectronauttoMSstatsFormat(input,
      summaryforMultipleRows=max)	

Arguments

input	name of Spectronaut output, which is long-format. ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity, F.ExcludedFromQuantification are required. Rows with F.ExcludedFromQuantification=True will be removed.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.

Author(s)

Meena Choi, Olga Vitek. 

and I was wondering what it does and which input (Spectronaut Report) it actually expects. There is indeed a Spectronaut export scheme for MSstats, but the contained data is already collapsed on the peptide level (no fragment level AUC), so not really what one would like to use according to Olga. Is anyone of you in contact with Biognosys? Since Spectronaut 10 there is also a MSstats fragment ion report, but the export scheme did not work when I tested it recently. Would be great if you could start talking to each other, regarding I/O formats. I used MSstats together with Spectronaut output twice and each time it took a considerable amount of time to transit the data. Would be great if this could be made easier in the future.

Greetings,

Tobi

[Meena Choi]

Msstats team is working with biognosys and is updating the function for converting spectronaut output for msstats input format. We are expecting to publish nes version of msstats within this week. Hope to help.

-Meena

[Tobias Kockmann]

Hi Meena,

I am still unable to process fragment ion level data exported from Spectronaut 10. What is the current situation regarding the parsing function or customized reporting schemes in Spectronaut?

Greetings,

Tobi

[Meena Choi]

Dear Tobi,

I just released MSstats 3.7.3. Please check user manual for v 3.7.3, especially from p. 47 for Spectronaut output.

Hope that it helps.

Sincerely,

- Meena