Supplementary Dataset 7

Chigumba, Desnor

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Work Description

Title: Supplementary Dataset 7 Tombstone Deposited

Attribute	Value
Methodology	Database Search with MSFragger on FragPipe For MSFragger database searches, Fragpipe v19.1 was used as the search engine. Additional configurations were as follows: MSFragger v4.0 software, IonQuant v1.10.12, Philosopher v5.1.0 and, EasyPQP 0.1.42. Closed search: The default workflow was used with the precursor and fragment ion mass tolerance set to 20 PPM. Mass calibration and parameter optimization were enabled with allowed isotope error 0/1/2. For AhyBURP-WT, CcaBURP1-[1xQILFW], and SkrBURP-[1xVLFYPSY] , trypsin was selected as the digestive enzyme while AspN was selected for KjaBURP. A maximum number of two missed cleavages was allowed, and the minimum and maximum peptide length was set to 7 and 50, respectively, except for AspN digestions which were set to 6 and 55. The peptide mass range was set to 500 to 5000 Da. Methionine oxidation, N-terminal acetylation were selected as dynamic modifications. For peptide validation, PSM validation was conducted using Percolator with Protein Prophet and FDR filter was set to 0.01. For in vitro samples, the reference database used comprised of the respective protein sequence listed in Supplementary Information. For plant samples, in addition to the above-mentioned dynamic modifications, cysteine carbamidomethylation was speciﬁed as a ﬁxed modiﬁcation. In addition, the reference database was comprised of the respective sequence for the protein interest as well as a list of N. benthamiana proteins obtained from UniProt(Taxonomy ID:4100). Decoy proteins were generated by reversing the target proteins in FragPipe. Cyclization massoffset search: The massoffset was used with the same parameters listed above for the closed search. However, under advanced options, mass offsets were set to 0, -1.00078, -2.10158, -3.02352, -4.03136 and the delta mass restriction was set to “all” so that any amino acid with the delta mass would be identified.
Description	Database Search with MSFragger on FragPipe
Creator	Chigumba, Desnor
Creator ORCID iD	https://orcid.org/0000-0001-9785-5432
Depositor	[email protected]
Contact information	[email protected]
Discipline	Science
Keyword	MSFragger, proteomics, BURP domain
Date coverage	2023 to 2024
Resource type	Dataset
Last modified	10/10/2024
Published	10/10/2024
Language	English
DOI	https://doi.org/10.7302/ba8q-m396
Ticket	https://teamdynamix.umich.edu/TDNext/Apps/87/Tickets/TicketDet?TicketID=6258345
License	http://creativecommons.org/licenses/by-nc/4.0/
View Users	[email protected]
Edit Users	[email protected]
View Groups	public
View Groups	admin

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