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High-resolution quadrupole improves spectral purity and reduces interference from non-target ions in isobaric multiplexed quantitative proteomics.
Zhang, Shen; Le Blanc, J C Yves; Larsen, Brett; Colwill, Karen; Burton, Lyle; Guna, Mircea; Gingras, Anne-Claude; Tate, Stephen.
Afiliación
  • Zhang S; SCIEX, Vaughan, Ontario, L4K 4V8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, M5G 1X5, Canada; NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 41
  • Le Blanc JCY; SCIEX, Vaughan, Ontario, L4K 4V8, Canada.
  • Larsen B; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, M5G 1X5, Canada.
  • Colwill K; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, M5G 1X5, Canada.
  • Burton L; SCIEX, Vaughan, Ontario, L4K 4V8, Canada.
  • Guna M; SCIEX, Vaughan, Ontario, L4K 4V8, Canada.
  • Gingras AC; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1X8, Canada. Electronic address: gingras@lunenfeld.ca.
  • Tate S; SCIEX, Vaughan, Ontario, L4K 4V8, Canada. Electronic address: Stephen.Tate@sciex.com.
Anal Chim Acta ; 1325: 343135, 2024 Oct 09.
Article en En | MEDLINE | ID: mdl-39244297
ABSTRACT

BACKGROUND:

Mass spectrometry (MS)-based proteomics is a powerful tool for identifying and quantifying proteins. However, chimeric spectra caused by the fragmentation of multiple precursors within the same isolation window impair the accuracy of peptide identification and isobaric mass tag-based quantification. While there have been advances in computational deconvolution of chimeric spectra and methods to further separate the peptides by ion mobility or through MSn, the use of narrower isolation windows to decrease the fraction of chimeric species remains to be fully explored.

RESULTS:

We present results obtained on a SCIEX TripleTOF instrument where the quadrupole was optimized and tuned for precursor isolation at 0.1 Da (FWHH). Using a three-proteome model (trypsin digest of protein lysates from yeast, human and E. coli) and 8-plex iTRAQ labeling to document the interference effect, we investigated the impact of co-fragmentation on spectral purity, identification accuracy and quantification accuracy. The narrow quadrupole isolation window significantly improved the spectral purity and reduced the interference of non-target precursors on quantification accuracy. The high-resolution isolation strategy also reduced the number of false identifications caused by chimeric spectra. While these improvements came at the cost of sensitivity loss, combining high-resolution isolation with other advanced techniques, including ion mobility, may result in improved accuracy in identification and quantification.

SIGNIFICANCE:

Compared to standard-resolution quadrupole isolation (0.7 Da), high-resolution quadrupole isolation (0.1 Da) significantly improved the spectral purity and quantification accuracy while reducing the number of potential false identifications caused by chimeric spectra, thus showing excellent potential for further development to analyze clinical proteomics samples, for which high accuracy is essential.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteómica Límite: Humans Idioma: En Revista: Anal Chim Acta Año: 2024 Tipo del documento: Article Pais de publicación: Países Bajos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteómica Límite: Humans Idioma: En Revista: Anal Chim Acta Año: 2024 Tipo del documento: Article Pais de publicación: Países Bajos