International Journal of Proteomics

Research Article

Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions

Table 1

Phosphorylated and acetylated ErbB2 peptides identified and quantified by SWATH MS2. Modifications include phosphorylation +80, acetylation +42, and oxidation +16.


Peptide	SWATH %CV	Modified residue	Enzyme		Fragment ion

DPPERGAPPSTFKGT[+80]PTA	15.9%	1240	Asp-N	3	b7
DVRPQPPS[+80]PR	10.9%	1151	Asp-N	3	b5
EGPLPAARPAGAT[+80]LERPK	12.4%	1166	Trypsin	2	y14
ERPKTLS[+80]PGKNGVVK	24.8%	1174	Asp-N	4	y4
GAPPSTFKGT[+80]PTA	25.1%	1240	Trypsin + Asp-N	2	y3
GLQS[+80]LPTHDPSPLQR	26.6%	1100	Trypsin	3	b4
K[+42]GTPTAENPEYLGLDVPV	23.7%	1238	Chymotrypsin	2	b11
KGT[+80]PTAENPEYLGLDVPV	18.5%	1240	Chymotrypsin	3	b8
LLQETELVEPLT[+80]PSGAM[+16]PNQAQM[+16]R	22.9%	701	Trypsin + Asp-N	3	y12
LLQETELVEPLT[+80]PSGAM[+16]PNQAQMR	30.1%	701	Trypsin	3	b8
LLQETELVEPLT[+80]PSGAMPNQAQM[+16]R	30.8%	701	Trypsin	3	b8
LLQETELVEPLT[+80]PSGAM[+16]PNQAQM[+16]R	20.4%	701	Trypsin	3	y12
PAGAT[+80]LERPK	18.7%	1166	Trypsin	2	y6
S[+80]GGGDLTLGLEPSEEEAPR	30.8%	1154	Trypsin	3	y8
SPLAPSEGAGS[+80]DVFDGDLGM[+16]GAAK	54.5%	1082	Trypsin	3	y10
TLS[+80]PGKNGVVK	18.9%	1174	Trypsin	2	y9