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Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.

Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R.

Nat Biotechnol. 2017 Aug;35(8):781-788. doi: 10.1038/nbt.3908. Epub 2017 Jun 12.


Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry.

Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R.

Mol Cell Proteomics. 2015 Oct;14(10):2800-13. doi: 10.1074/mcp.O114.042267. Epub 2015 Jul 21.


Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides.

Sidoli S, Fujiwara R, Garcia BA.

Proteomics. 2016 Aug;16(15-16):2095-105. doi: 10.1002/pmic.201500527. Epub 2016 Jun 8.


Confident phosphorylation site localization using the Mascot Delta Score.

Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B.

Mol Cell Proteomics. 2011 Feb;10(2):M110.003830. doi: 10.1074/mcp.M110.003830. Epub 2010 Nov 6.


Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications.

Sidoli S, Lin S, Xiong L, Bhanu NV, Karch KR, Johansen E, Hunter C, Mollah S, Garcia BA.

Mol Cell Proteomics. 2015 Sep;14(9):2420-8. doi: 10.1074/mcp.O114.046102. Epub 2015 Jan 30.


Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry.

Krautkramer KA, Reiter L, Denu JM, Dowell JA.

J Proteome Res. 2015 Aug 7;14(8):3252-62. doi: 10.1021/acs.jproteome.5b00245. Epub 2015 Jul 13.


DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI.

Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255. Epub 2015 Jan 19.


Technical advances in proteomics: new developments in data-independent acquisition.

Hu A, Noble WS, Wolf-Yadlin A.

F1000Res. 2016 Mar 31;5. pii: F1000 Faculty Rev-419. doi: 10.12688/f1000research.7042.1. eCollection 2016. Review.


Computational Methods in Mass Spectrometry-Based Proteomics.

Li S, Tang H.

Adv Exp Med Biol. 2016;939:63-89. Review.


Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry.

Li S, Cao Q, Xiao W, Guo Y, Yang Y, Duan X, Shui W.

J Proteome Res. 2017 Feb 3;16(2):738-747. doi: 10.1021/acs.jproteome.6b00767. Epub 2017 Jan 3.


Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry.

Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R.

Mol Cell Proteomics. 2015 Mar;14(3):739-49. doi: 10.1074/mcp.M113.035550. Epub 2015 Jan 5.


Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS.

Liu Y, Hüttenhain R, Surinova S, Gillet LC, Mouritsen J, Brunner R, Navarro P, Aebersold R.

Proteomics. 2013 Apr;13(8):1247-56. doi: 10.1002/pmic.201200417. Epub 2013 Mar 11.


Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.

Collins MO, Wright JC, Jones M, Rayner JC, Choudhary JS.

J Proteomics. 2014 May 30;103:1-14. doi: 10.1016/j.jprot.2014.03.010. Epub 2014 Mar 21.


Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics-a prototype design for a single injection assay.

Heaven MR, Funk AJ, Cobbs AL, Haffey WD, Norris JL, McCullumsmith RE, Greis KD.

J Mass Spectrom. 2016 Jan;51(1):1-11. doi: 10.1002/jms.3716.


Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications.

Sidoli S, Simithy J, Karch KR, Kulej K, Garcia BA.

Anal Chem. 2015 Nov 17;87(22):11448-54. doi: 10.1021/acs.analchem.5b03009. Epub 2015 Nov 5.


Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R.

Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. doi: 10.1074/mcp.O111.016717. Epub 2012 Jan 18.


Simultaneous quantification of protein phosphorylation sites using liquid chromatography-tandem mass spectrometry-based targeted proteomics: a linear algebra approach for isobaric phosphopeptides.

Xu F, Yang T, Sheng Y, Zhong T, Yang M, Chen Y.

J Proteome Res. 2014 Dec 5;13(12):5452-60. doi: 10.1021/pr500339u. Epub 2014 Nov 17.


Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms.

Röst HL, Aebersold R, Schubert OT.

Methods Mol Biol. 2017;1550:289-307. doi: 10.1007/978-1-4939-6747-6_20.


A repository of assays to quantify 10,000 human proteins by SWATH-MS.

Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R.

Sci Data. 2014 Sep 16;1:140031. doi: 10.1038/sdata.2014.31. eCollection 2014.


Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides.

Keller A, Bader SL, Kusebauch U, Shteynberg D, Hood L, Moritz RL.

Mol Cell Proteomics. 2016 Mar;15(3):1151-63. doi: 10.1074/mcp.M115.054478. Epub 2015 Dec 24.

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