MassIVE MSV000095427

Complete Public PXD054173

LINE-1 ORF1p co-immunoprecipitations analyzed by DDA and two DIA methods

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Description

Using an anti-ORF1 monoclonal (clone 4H1; Milipore), four co-immunoprecipitations to enrich for LINE-1 ORF1p and its interactors as described in Di Stefano, L.H. et al. (https://doi.org/10.1007/978-1-0716-2883-6_12), from either HEK-293TLD (cells transfected with pMT646- containing a L1 sequence) or N2102Ep (embryonal carcinoma cells with endogenous expression of LINE-1) lysates were then analyzed in DDA, HRMS1, and Variable Window modes. Mouse polyclonal IgG were used as mock IPs as nonspecific binding controls. MMTS alkylated the cysteines. DDA and Variable Window experiments collected spectra for 60 minutes of the one hour run time. The HRMS1 experiments collected spectra for 90 minutes of a two hour run time. The UP000005640 reference proteome for Homo sapiens, including unreviewed sequences and reviewed isoforms was used as a search space (104,558 sequences) [doi:10.25345/C51N7XZ74] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: co-immunoprecipitation ; data-independent acquisition ; LINE-1

Contact

Principal Investigators:
(in alphabetical order) 		John P. LaCava, University of Groningen, Netherlands
Submitting User: dtabb73

Publications

Tabb DL, Kaniyar MH, Bringas OGR, Shin H, Di Stefano L, Taylor MS, Xie S, Yilmaz OH, LaCava J.
Interrogating data-independent acquisition LC-MS/MS for affinity proteomics.
J Proteins Proteom. 2024;15(3):281-298. Epub 2024 Sep 17.

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