ISA-Tab annotation for the "SARS-CoV-2 infected host cell proteomics reveal potential therapy targets" publication

This is part of an effort to (re-)annotate

https://dx.doi.org/10.21203/rs.3.rs-17218/v1

Proteomics data

Available from PRIDE at https://www.ebi.ac.uk/pride/archive/projects/PXD017710 and MassIVE/CCMS Maestro+MSstats reanalysis of MSV000085096 / PXD017710

ISA-Tab

The formatting and reannotation are based on information extracted from:

• the original publication
• the supplementary tables available from the publishers site
• the 'filtered-results.csv' helper file as supplied to @sneumann during the HUPO-PSI

Viewing the ISA-tab formatted and reannotated PXD017710 with ISATab-Viewer

Viewing the ISA-tab formatted and reannotated PXD017710 locally, do the following:

python -m http.server 8000

Then point your browser to http://0.0.0.0:8000/isaviewer-demo.html

Task performed:

• initial structure of the study design in ISA format:

• linkage of Proteome and Translatome data (supplementary material) to ISA assay tables (via Derived Data File)

• processing the Proteome and Translatome data (supplementary material) with python pandas library to generate the following csv files:

  • proteome_intensities_long_table_ggplot2.txt
  • proteome_diffanal_ratio_pvalue_long_table_ggplot2.txt
  • translatome_intensities_long_table_ggplot2.txt
  • translatome_diffanal_ratio_pvalue_long_table_ggplot2

  The files are long table corresponding to a melt on the Excel file originally generated by the users and can be readily loaded in R ggplot2 library for graphical representation. The statistical relevant elements have been annotated with the STATO ontology and the tables comply with a Frictionless.io Data Package. The jupyter notebook for the transformation is available.

• conversion of raw data to mzML format

install docker:

		>brew update
		>brew install docker

sign in to docker

		>docker start
		>docker login

pull docker container for ProteoWizard:

>docker pull chambm/pwiz-i-agree-to-the-vendor-licenses

⚠️ be sure to sign-up and login to https://hub.docker.com/

in order to be able to reach

https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses

run the pwiz tool from the container over the raw data:

 docker run -it --rm -e WINEDEBUG=-all -v /Users/philippe/Downloads/PXD017710/raw/:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/*.raw --mzML

• ontology markup for:
  • declaration of independant variables as ISA Study Factors:{biological agent, dose, timepoint,replicate} ->OBI
  • Taxonomic information (host cells and virus) -> NCBITaxonomy
  • Cell line: CaCo-2 cells -> Cell Line Ontology
  • Disease: Colon Cancer -> Human Phenotype Ontology
  • MS specific aspect (TMT reagent, instrument ... ) -> PSI-MS
  • Statistical Tests -> STATO

unresolved curatorial issues:

1. ambiguities related to Tandem Mass Tag labeling protococol

   • the publication mentions TMT11 (see Figure 2 in https://www.researchsquare.com/article/rs-17218/v1)
   • the information available from PRIDE mentions TMT6 (https://www.ebi.ac.uk/pride/archive/projects/PXD017710) This may require another round of annotation on the TMT agents and fractions in the ISA a_assay representation

2. SARS-Cov2 isolate: no clear NCBI Taxonomic anchoring and unclear origin: -> the markup is made to the parent class (as of 06.04.2020)

validation with ISA API:

The default ISA configuration from https://isa-tools.org/format/configurations/index.html was used for validation.

Code snipet showing how to invoke the python ISA validator from the isatools API

import isatools
import os
from isatools import isatab

my_json_report = isatab.validate(open(os.path.join('PXD017710', 'i_PXD017710.txt')))

print(my_json_report)

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FAIRification Objectives, Inputs and Outputs

Actions.Objectives.Tasks	Input	Output
validation	Investigation Study Assay (ISA)	report
formatting	tab delimited file	Investigation Study Assay (ISA)
formatting	Waters MS format	mzML
text annotation	CLO	annotated text
text annotation	OBI	annotated text
text annotation	NCBI taxonomy	annotated text
text annotation	HP	annotated text
text annotation	MS	annotated text

Table of Data Standards

Data Formats	Terminologies	Models
Investigation Study Assay (ISA)	CLO
mzML	OBI
	NCBI taxonomy
	HP
	MS
	STATO

Authors:

Name	Affiliation	orcid	CrediT role
Steffen Neumann	IPB-Halle	0000-0002-7899-7192	Writing - First Draft
Philippe Rocca-Serra	Data Readiness Group, Department of Engineering Science, University of Oxford,	0000-0001-9853-5668	Writing - Review

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License: