MassIVE MSV000090624

Partial Public

IP-LC/MS pulldown assay for identifying TFPI2-associated membrane protein in human primary microglia

Description

IP-LC/MS pulldown assay for identifying TFPI2-associated membrane protein in human primary microglia. Tandem mass spectra were extracted. Charge state deconvolution and deisotoping were not performed. All MS/MS samples were analyzed using Mascot (Matrix Science, London, UK; version 2.8.0). Mascot was set up to search the uniprot-SP-human_20190906_20200629 database (20432 entries) assuming the digestion enzyme trypsin. Mascot was searched with a fragment ion mass tolerance of 0.050 Da and a parent ion tolerance of 10.0 PPM. Carbamidomethyl of cysteine was specified in Mascot as a fixed modification. Deamidated of asparagine and glutamine, oxidation of methionine and acetyl of the n-terminus were specified in Mascot as variable modifications. Scaffold (version Scaffold_5.1.2, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. Peptide identifications were accepted if they could be established at greater than 90.0% probability by the Peptide Prophet algorithm (Keller, A et al Anal. Chem. 2002;74(20):5383-92) with Scaffold delta-mass correction. Protein identifications were accepted if they could be established at greater than 99.0% probability to achieve an FDR less than 1.0% and contained at least 2 identified peptides. Protein probabilities were assigned by the Protein Prophet algorithm (Nesvizhskii, Al et al Anal. Chem. 2003;75(17):4646-58). Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. Sample #3 is protein eluted from the complex containing TFPI2 antibody. Sample #4 is IgG control. [doi:10.25345/C5CR5NH6W] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: TFPI2, Microglia, Glioblastoma

Contact

Principal Investigators:
(in alphabetical order)
Peiwen Chen, Northwestern University, US
Submitting User: Lizhi
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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.