-
Something wrong with this record ?
Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues
J. Faktor, R. Sucha, V. Paralova, Y. Liu, P. Bouchal,
Language English Country Germany
Document type Comparative Study, Journal Article
- MeSH
- Mass Spectrometry instrumentation methods MeSH
- Humans MeSH
- Limit of Detection MeSH
- Neoplasms chemistry metabolism MeSH
- Signal-To-Noise Ratio MeSH
- Proteins analysis MeSH
- Proteomics methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Comparative Study MeSH
Targeted mass spectrometry-based proteomics approaches enable the simultaneous and reproducible quantification of multiple protein analytes across numerous conditions in biology and clinical studies. These approaches involve e.g. selected reaction monitoring (SRM) typically conducted on a triple quadrupole mass spectrometer, its high-resolution variant named pseudo-SRM (p-SRM), carried out in a quadrupole coupled with an TOF analyzer (qTOF), and "sequential window acquisition of all theoretical spectra" (SWATH). Here we compared these methods in terms of signal-to-noise ratio (S/N), coefficient of variance (CV), fold change (FC), limit of detection and quantitation (LOD, LOQ). We have shown the highest S/N for p-SRM mode, followed by SRM and SWATH, demonstrating a trade-off between sensitivity and level of multiplexing for SRM, p-SRM, and SWATH. SRM was more sensitive than p-SRM based on determining their LOD and LOQ. Although SWATH has the worst S/N, it enables peptide multiplexing with post-acquisition definition of the targets, leading to better proteome coverage. FC between breast tumors of different clinical-pathological characteristics were highly correlated (R2 >0.97) across three methods and consistent with the previous study on 96 tumor tissues. Our technical note presented here, therefore, confirmed that outputs of all the three methods were biologically relevant and highly applicable to cancer research.
Department of Biochemistry Faculty of Science Masaryk University Brno Czech Republic
Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
Regional Centre for Applied Molecular Oncology Masaryk Memorial Cancer Institute Brno Czech Republic
References provided by Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc18016865
- 003
- CZ-PrNML
- 005
- 20190204090553.0
- 007
- ta
- 008
- 180515s2017 gw f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1002/pmic.201600323 $2 doi
- 035 __
- $a (PubMed)27966270
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a gw
- 100 1_
- $a Faktor, Jakub $u Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
- 245 10
- $a Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues / $c J. Faktor, R. Sucha, V. Paralova, Y. Liu, P. Bouchal,
- 520 9_
- $a Targeted mass spectrometry-based proteomics approaches enable the simultaneous and reproducible quantification of multiple protein analytes across numerous conditions in biology and clinical studies. These approaches involve e.g. selected reaction monitoring (SRM) typically conducted on a triple quadrupole mass spectrometer, its high-resolution variant named pseudo-SRM (p-SRM), carried out in a quadrupole coupled with an TOF analyzer (qTOF), and "sequential window acquisition of all theoretical spectra" (SWATH). Here we compared these methods in terms of signal-to-noise ratio (S/N), coefficient of variance (CV), fold change (FC), limit of detection and quantitation (LOD, LOQ). We have shown the highest S/N for p-SRM mode, followed by SRM and SWATH, demonstrating a trade-off between sensitivity and level of multiplexing for SRM, p-SRM, and SWATH. SRM was more sensitive than p-SRM based on determining their LOD and LOQ. Although SWATH has the worst S/N, it enables peptide multiplexing with post-acquisition definition of the targets, leading to better proteome coverage. FC between breast tumors of different clinical-pathological characteristics were highly correlated (R2 >0.97) across three methods and consistent with the previous study on 96 tumor tissues. Our technical note presented here, therefore, confirmed that outputs of all the three methods were biologically relevant and highly applicable to cancer research.
- 650 _2
- $a lidé $7 D006801
- 650 _2
- $a limita detekce $7 D057230
- 650 _2
- $a hmotnostní spektrometrie $x přístrojové vybavení $x metody $7 D013058
- 650 _2
- $a nádory $x chemie $x metabolismus $7 D009369
- 650 _2
- $a proteiny $x analýza $7 D011506
- 650 _2
- $a proteomika $x metody $7 D040901
- 650 _2
- $a poměr signál - šum $7 D059629
- 655 _2
- $a srovnávací studie $7 D003160
- 655 _2
- $a časopisecké články $7 D016428
- 700 1_
- $a Sucha, Rita $u Laboratory of Applied Proteome Analyses and Research Center PIGMOD, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Libechov, Czech Republic.
- 700 1_
- $a Paralova, Vendula $u Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
- 700 1_
- $a Liu, Yansheng $u Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- 700 1_
- $a Bouchal, Pavel, $u Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic. Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic. $d 1975- $7 xx0128495
- 773 0_
- $w MED00007044 $t Proteomics $x 1615-9861 $g Roč. 17, č. 5 (2017)
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/27966270 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y a $z 0
- 990 __
- $a 20180515 $b ABA008
- 991 __
- $a 20190204090830 $b ABA008
- 999 __
- $a ok $b bmc $g 1300489 $s 1013705
- BAS __
- $a 3
- BAS __
- $a PreBMC
- BMC __
- $a 2017 $b 17 $c 5 $e 20170222 $i 1615-9861 $m Proteomics $n Proteomics $x MED00007044
- LZP __
- $a Pubmed-20180515
