In mass spectrometry, data-independent acquisition (DIA) is a method of molecular structure determination in which all ions within a selected m/z range are fragmented and analyzed in a second stage of tandem mass spectrometry.[1][2] Tandem mass spectra are acquired either by fragmenting all ions that enter the mass spectrometer at a given time (called broadband DIA) or by sequentially isolating and fragmenting ranges of m/z.[3] DIA is an alternative to data-dependent acquisition (DDA) where a fixed number of precursor ions are selected and analyzed by tandem mass spectrometry.
MSE is a broadband DIA technique that uses alternating low-energy CID and high-energy CID. The low-energy CID is used to acquire precursor ion mass spectra whereas the high-energy CID is used to obtain product ion information by tandem mass spectrometry.[5]
Data analysisedit
Data analysis is generally challenging for DIA methods as the resulting fragment ion spectra are highly multiplexed. In DIA spectra therefore the direct relation between a precursor ion and its fragment ions is lost since the fragment ions in DIA spectra may potentially result from multiple precursor ions (any precursor ion present in the m/z range from which the DIA spectrum was derived).
One approach to DIA data analysis attempts to use database-based search engines used in data-dependent acquisition to search the produced multiplexed spectra.[4][6] This approach can be improved by assigning individual fragment ion to precursor ions observed in precursor ion scans, using the elution profile of the fragment ions and the precursor ions, and then searching the resulting "pseudo-spectra".[5]
A second approach to DIA data analysis is based on a targeted analysis, also known as SWATH-MS (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra).[7] This approach uses targeted extraction of fragment ion traces directly for identification and quantification without an explicit attempt to de-multiplex the DIA fragment ion spectra.
^Law, Kai Pong; Lim, Yoon Pin (2014). "Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring". Expert Review of Proteomics. 10 (6): 551–566. doi:10.1586/14789450.2013.858022. ISSN 1478-9450. PMID 24206228. S2CID 29969570.
^Chapman, John D.; Goodlett, David R.; Masselon, Christophe D. (2014). "Multiplexed and data-independent tandem mass spectrometry for global proteome profiling". Mass Spectrometry Reviews. 33 (6): 452–470. Bibcode:2014MSRv...33..452C. doi:10.1002/mas.21400. ISSN 0277-7037. PMID 24281846.
^ abPurvine, Samuel; Eppel, Jason-Thomas; Yi, Eugene C.; Goodlett, David R. (2003). "Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer". Proteomics. 3 (6): 847–850. doi:10.1002/pmic.200300362. ISSN 1615-9853. PMID 12833507. S2CID 31639003.
^ abcPlumb, Robert S.; Johnson, Kelly A.; Rainville, Paul; Smith, Brian W.; Wilson, Ian D.; Castro-Perez, Jose M.; Nicholson, Jeremy K. (2006). "UPLC/MSE; a new approach for generating molecular fragment information for biomarker structure elucidation". Rapid Communications in Mass Spectrometry. 20 (13): 1989–1994. Bibcode:2006RCMS...20.1989P. doi:10.1002/rcm.2550. ISSN 0951-4198. PMID 16755610.
^Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR (2004). "Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra". Nat. Methods. 1 (1): 39–45. doi:10.1038/nmeth705. PMID 15782151. S2CID 9780065.
^Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R (2012). "Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis". Mol. Cell. Proteomics. 11 (6): O111.016717. doi:10.1074/mcp.O111.016717. PMC3433915. PMID 22261725.
Further readingedit
Bilbao, Aivett; Varesio, Emmanuel; Luban, Jeremy; Strambio-De-Castillia, Caterina; Hopfgartner, Gérard; Müller, Markus; Lisacek, Frédérique (2015). "Processing strategies and software solutions for data-independent acquisition in mass spectrometry". Proteomics. 15 (5–6): 964–980. doi:10.1002/pmic.201400323. ISSN 1615-9853. PMID 25430050. S2CID 24822571.
January 01, 1970
data, independent, acquisition, mass, spectrometry, data, independent, acquisition, method, molecular, structure, determination, which, ions, within, selected, range, fragmented, analyzed, second, stage, tandem, mass, spectrometry, tandem, mass, spectra, acqui. In mass spectrometry data independent acquisition DIA is a method of molecular structure determination in which all ions within a selected m z range are fragmented and analyzed in a second stage of tandem mass spectrometry 1 2 Tandem mass spectra are acquired either by fragmenting all ions that enter the mass spectrometer at a given time called broadband DIA or by sequentially isolating and fragmenting ranges of m z 3 DIA is an alternative to data dependent acquisition DDA where a fixed number of precursor ions are selected and analyzed by tandem mass spectrometry Contents 1 Broadband 2 Data analysis 3 See also 4 References 5 Further readingBroadband editOne of the first DIA approaches was a nozzle skimmer dissociation method called shotgun collision induced dissociation CID 4 5 Fragmentation can be in the ion source of the mass spectrometer by increasing the nozzle skimmer voltage in electrospray ionization MSE is a broadband DIA technique that uses alternating low energy CID and high energy CID The low energy CID is used to acquire precursor ion mass spectra whereas the high energy CID is used to obtain product ion information by tandem mass spectrometry 5 Data analysis editData analysis is generally challenging for DIA methods as the resulting fragment ion spectra are highly multiplexed In DIA spectra therefore the direct relation between a precursor ion and its fragment ions is lost since the fragment ions in DIA spectra may potentially result from multiple precursor ions any precursor ion present in the m z range from which the DIA spectrum was derived One approach to DIA data analysis attempts to use database based search engines used in data dependent acquisition to search the produced multiplexed spectra 4 6 This approach can be improved by assigning individual fragment ion to precursor ions observed in precursor ion scans using the elution profile of the fragment ions and the precursor ions and then searching the resulting pseudo spectra 5 A second approach to DIA data analysis is based on a targeted analysis also known as SWATH MS Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra 7 This approach uses targeted extraction of fragment ion traces directly for identification and quantification without an explicit attempt to de multiplex the DIA fragment ion spectra See also editFragmentation mass spectrometry Ion mobility spectrometry mass spectrometry Targeted mass spectrometryReferences edit Doerr Allison 2014 DIA mass spectrometry Nature Methods 12 1 35 doi 10 1038 nmeth 3234 ISSN 1548 7091 S2CID 83712891 Law Kai Pong Lim Yoon Pin 2014 Recent advances in mass spectrometry data independent analysis and hyper reaction monitoring Expert Review of Proteomics 10 6 551 566 doi 10 1586 14789450 2013 858022 ISSN 1478 9450 PMID 24206228 S2CID 29969570 Chapman John D Goodlett David R Masselon Christophe D 2014 Multiplexed and data independent tandem mass spectrometry for global proteome profiling Mass Spectrometry Reviews 33 6 452 470 Bibcode 2014MSRv 33 452C doi 10 1002 mas 21400 ISSN 0277 7037 PMID 24281846 a b Purvine Samuel Eppel Jason Thomas Yi Eugene C Goodlett David R 2003 Shotgun collision induced dissociation of peptides using a time of flight mass analyzer Proteomics 3 6 847 850 doi 10 1002 pmic 200300362 ISSN 1615 9853 PMID 12833507 S2CID 31639003 a b c Plumb Robert S Johnson Kelly A Rainville Paul Smith Brian W Wilson Ian D Castro Perez Jose M Nicholson Jeremy K 2006 UPLC MSE a new approach for generating molecular fragment information for biomarker structure elucidation Rapid Communications in Mass Spectrometry 20 13 1989 1994 Bibcode 2006RCMS 20 1989P doi 10 1002 rcm 2550 ISSN 0951 4198 PMID 16755610 Venable JD Dong MQ Wohlschlegel J Dillin A Yates JR 2004 Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra Nat Methods 1 1 39 45 doi 10 1038 nmeth705 PMID 15782151 S2CID 9780065 Gillet LC Navarro P Tate S Rost H Selevsek N Reiter L Bonner R Aebersold R 2012 Targeted data extraction of the MS MS spectra generated by data independent acquisition a new concept for consistent and accurate proteome analysis Mol Cell Proteomics 11 6 O111 016717 doi 10 1074 mcp O111 016717 PMC 3433915 PMID 22261725 Further reading editBilbao Aivett Varesio Emmanuel Luban Jeremy Strambio De Castillia Caterina Hopfgartner Gerard Muller Markus Lisacek Frederique 2015 Processing strategies and software solutions for data independent acquisition in mass spectrometry Proteomics 15 5 6 964 980 doi 10 1002 pmic 201400323 ISSN 1615 9853 PMID 25430050 S2CID 24822571 Retrieved from https en wikipedia org w index php title Data independent acquisition amp oldid 1216371208, wikipedia, wiki, book, books, library,
