Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

Table 4 Phosphopeptide counts

Protein	Number of distinct identified phosphorylation sites	Location of phospho sites	Number of contributing PSMs
N	20	S2, S105, T141, S176, S180, S183, S184, T391, S78, S79, T76, S206, T205, S23, T24, T166, S194, S201, S202, T198	74
M	5	S211, S212, T208, S213, S214	43
S glycoprotein	13	S1261, S1161, S1196, T791, Y789, S459, S816, S349, T240, S31, T29, S637, S640	21
nsp3	5	S794, S661, T504, S1826, S660	16
ORF 3a	0	QGEIKDATPSDFVR	1
nsp9	1	S5	1
nsp12	0	GFFKEGSSVELK	1

Listed for each protein is the number of distinct phospho sites identified along with the locations and amino acid modified as well as how many contributing PSMs there are in total. Each named site has confidence of at least 70% as defined by the PhosphoRS node of Proteome Discoverer software. For proteins ORF3a and nsp12, no distinct site could be identified despite a phosphorylated peptide being found; in these cases, the peptide sequence is provided

ISSN: 1756-994X