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Investigation Description Format

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Marie Locard-Paulet edited this page Jul 8, 2021 · 6 revisions

The MAGE-TAB is composed of two main files SDRF and IDF. The IDF - investigation description format aims to capture the general description of the experiment and dataset. Similar to the exiting ProteomeXchange.xml, the IDF capture information about title of the experiment, a general description, or the submitter information.

Example IDF:

MAGE-TAB Version	1.1
Investigation Title	Ultra-deep human phosphoproteome
Experiment Description	Regulatory protein phosphorylation controls nearly every normal and pathophysiological signaling system in eukaryotic cells. Despite great advances in mass spectrometry based-proteomics, the total number, localization and site-specific stoichiometry of this post-translational modification (PTM) are unknown. 

Date of Experiment	2014-08-06
Public Release Date	2014-08-06

Protocol Name	P-MTAB-Sample-PXD000612	P-MTAB-Data-PXD000612
Protocol Type	sample collection protocol	data analysis protocol
Protocol Description	HeLa S3 cells were subjected to a double thymidine block in combination with nocodazole to obtain a homogenous mitotic phase population and the efficiency of mitotic arrest was monitored by FACS analysis.	Raw mass spectrometric data was analyzed in the MaxQuant environment version 1.5.0.0, and employed Andromeda for database search. The MS/MS spectra were matched against the human Uniprot FASTA database version 2/25/2012 (81213 entries). Enzyme specificity was set to trypsin and the search included cysteine carbamidomethylation as a fixed modification and N-acetylation of protein, oxidation of methionine and/or phosphorylation of Ser, Thr, Tyr residue (STY) as variable modifications. Up to two missed cleavages were allowed for protease digestion and peptides had to be fully tryptic.
Protocol Parameters
Protocol Hardware	Q Exactive
Protocol Software
Protocol Contact

Person Last Name	Oroshi	Mann
Person First Name	Mario	Matthias
Person Mid Initials
Person Email	[email protected]	[email protected]
Person Phone
Person Fax
Person Affiliation	Proteomics	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry
Person Address
Person Roles	submitter	principal investigator
Person Roles Term Source REF
Person Roles Term Accession Number

Experimental Factor Name	compound	enrichment process

SDRF File	PXD000612.sdrf.tsv
Comment[SDRF-Proteomics version]	1.1
Comment[TemplateType]	proteomics

Comment[ProteomeXchange accession number]	PXD000612

The IDF describes the project and experiment general characteristics :

  • The IDF should be compatible with the existing ProteomeXchange.xml.
  • The IDF is a Tab-delimited and key-value pair.

The IDF specification defines the main characteristics of the file format, including columns, values etc.

NOTE: By 2021, for ProteomeXchange submitters, the IDF is automatically generated from the submission.px.

Examples

PXD000612 - https://github.com/ypriverol/proteomics-metadata-standard/blob/master/annotated-projects/PXD000612/PXD000612.idf.tsv

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