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Statistical analysis of proteomic data of MPXV-infected HFF cells

YH Yiqi Huang
VB Valter Bergant
VG Vincent Grass
QE Quirin Emslander
MH M. Sabri Hamad
PH Philipp Hubel
JM Julia Mergner
AP Antonio Piras
KK Karsten Krey
AH Alexander Henrici
RÖ Rupert Öllinger
YT Yonas M. Tesfamariam
IR Ilaria Dalla Rosa
TB Till Bunse
GS Gerd Sutter
GE Gregor Ebert
FS Florian I. Schmidt
MW Michael Way
RR Roland Rad
AB Andrew G. Bowie
UP Ulrike Protzer
AP Andreas Pichlmair
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The model for HFF infection proteome can be represented by R GLM formula language as

where after(ti) effect represents the protein abundance change in mock condition between ti-1 and ti and is included in the model of all time points since ti; virus:after(ti) represents the MPXV-specific infection effect between ti-1 and ti. MS1peak is the log ratio of an MS1 peak intensity and the total protein abundance as described before23. The peak represents a peptide with a specific sequence, PTMs and charge, and the log ratio is assumed to be constant regardless of the experimental conditions110.

For any comparison between infected and mock samples to be valid, we required the protein group to be quantified in at least 50% of the replicates on either side of the comparison. A significant change at any given time was defined by |median log2 fold-change | ≥ 0.5 and p-value ≤ 10−2.

Copyright and License information: The Author(s) ©2024
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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