A systematic evaluation of chip-based nanoelectrospray parameters for rapid identification of proteins from a complex mixture
- PMID: 17689093
- DOI: 10.1016/j.jasms.2007.06.011
A systematic evaluation of chip-based nanoelectrospray parameters for rapid identification of proteins from a complex mixture
Abstract
HPLC-MS/MS is widely used for protein identification from gel spots and shotgun fractions. Although HPLC has well recognized benefits, this type of sample infusion also has some undesirable attributes: relatively low sample throughput, potential sample-to-sample carryover, time-varying sample composition, and no option for longer sample infusion for longer MS analyses. An automated chip-based ESI device (CB-ESI) has the potential to overcome these limitations. This report describes a systematic evaluation of the information-dependant acquisition (IDA) and sample preparation protocols for rapid protein identification from a complex mixture using a CB-ESI source compared with HPLC-ESI (gradient and isocratic elutions). Cytochrome c and a six-protein mixture (11-117 kDa) were used to develop an IDA protocol for rapid protein identification and to evaluate the effects of sample preparation protocols. MS (1-10 s) and MS/MS (1-60 s) scan times, sample concentration (50-500 fmol/microL), and ZipTipC(18) cleanup were evaluated. Based on MOWSE scores, protein coverage, experimental run time, number of identified proteins, and reproducibility, a 12.5 min experiment (22 cycles, each with one 3 s MS and eight 10 s MS/MS scans) was determined to be the optimal IDA protocol for CB-ESI. This work flow yielded up to 220% greater peptide coverage compared with gradient HPLC-ESI and provided protein identifications with up to a 2-fold higher throughput rate than either HPLC-ESI approach, whilst employing half the amount of sample over the same time frame. The results from this study support the use of CB-ESI as a rapid alternative to the identification of protein mixtures.
Similar articles
-
Rapid protein identification using direct infusion nanoelectrospray ionization mass spectrometry.Proteomics. 2006 Jan;6(1):16-25. doi: 10.1002/pmic.200500043. Proteomics. 2006. PMID: 16294305
-
Analysis of human hippocampus gangliosides by fully-automated chip-based nanoelectrospray tandem mass spectrometry.J Chromatogr A. 2006 Oct 20;1130(2):238-45. doi: 10.1016/j.chroma.2006.05.033. Epub 2006 Jun 23. J Chromatogr A. 2006. PMID: 16797567
-
Reprint of: chip-based nanoelectrospray mass spectrometry of brain gangliosides.Biochim Biophys Acta. 2011 Nov;1811(11):897-917. doi: 10.1016/j.bbalip.2011.09.006. Epub 2011 Sep 18. Biochim Biophys Acta. 2011. PMID: 21958495 Review.
-
Ultra-performance liquid chromatography/tandem mass spectrometric quantification of structurally diverse drug mixtures using an ESI-APCI multimode ionization source.Rapid Commun Mass Spectrom. 2007;21(6):893-902. doi: 10.1002/rcm.2908. Rapid Commun Mass Spectrom. 2007. PMID: 17295426
-
Chip-based nanoelectrospray mass spectrometry for protein characterization.Expert Rev Proteomics. 2004 Dec;1(4):449-68. doi: 10.1586/14789450.1.4.449. Expert Rev Proteomics. 2004. PMID: 15966841 Review.
Cited by
-
Rapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM).Anal Chem. 2022 Feb 1;94(4):1965-1973. doi: 10.1021/acs.analchem.1c03243. Epub 2022 Jan 19. Anal Chem. 2022. PMID: 35044165 Free PMC article.
-
Multi-Segment Direct Inject nano-ESI-LTQ-FT-ICR-MS/MS For Protein Identification.Proteome Sci. 2011 Jul 7;9:38. doi: 10.1186/1477-5956-9-38. Proteome Sci. 2011. PMID: 21736728 Free PMC article.
-
Label-Free Quantification from Direct Infusion Shotgun Proteome Analysis (DISPA-LFQ) with CsoDIAq Software.Anal Chem. 2023 Jan 17;95(2):677-685. doi: 10.1021/acs.analchem.2c02249. Epub 2022 Dec 17. Anal Chem. 2023. PMID: 36527718 Free PMC article.
-
Automated electrospray ionization FT-ICR mass spectrometry for petroleum analysis.J Am Soc Mass Spectrom. 2009 Feb;20(2):263-8. doi: 10.1016/j.jasms.2008.10.001. Epub 2008 Oct 9. J Am Soc Mass Spectrom. 2009. PMID: 18990588
-
Quantitative shotgun proteome analysis by direct infusion.Nat Methods. 2020 Dec;17(12):1222-1228. doi: 10.1038/s41592-020-00999-z. Epub 2020 Nov 23. Nat Methods. 2020. PMID: 33230323 Free PMC article.
References
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources