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Items: 1 to 20 of 113

1.

Clustering and filtering tandem mass spectra acquired in data-independent mode.

Pak H, Nikitin F, Gluck F, Lisacek F, Scherl A, Muller M.

J Am Soc Mass Spectrom. 2013 Dec;24(12):1862-71. doi: 10.1007/s13361-013-0720-z. Epub 2013 Sep 5.

PMID:
24006250
2.

Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry.

Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ.

Anal Chem. 2010 Feb 1;82(3):833-41. doi: 10.1021/ac901801b.

3.

High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples.

Madsen JA, Xu H, Robinson MR, Horton AP, Shaw JB, Giles DK, Kaoud TS, Dalby KN, Trent MS, Brodbelt JS.

Mol Cell Proteomics. 2013 Sep;12(9):2604-14. doi: 10.1074/mcp.O113.028258. Epub 2013 May 21.

4.

Clustering millions of tandem mass spectra.

Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA.

J Proteome Res. 2008 Jan;7(1):113-22. Epub 2007 Dec 8.

5.

ETISEQ--an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics.

Wong JW, Schwahn AB, Downard KM.

BMC Bioinformatics. 2009 Aug 10;10:244. doi: 10.1186/1471-2105-10-244.

6.

Chemical rule-based filtering of MS/MS spectra.

Reiz B, Kert├ęsz-Farkas A, Pongor S, Myers MP.

Bioinformatics. 2013 Apr 1;29(7):925-32. doi: 10.1093/bioinformatics/btt061. Epub 2013 Feb 15.

PMID:
23418188
7.

Applying 'Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra' (SWATH) for systematic toxicological analysis with liquid chromatography-high-resolution tandem mass spectrometry.

Arnhard K, Gottschall A, Pitterl F, Oberacher H.

Anal Bioanal Chem. 2015 Jan;407(2):405-14. doi: 10.1007/s00216-014-8262-1. Epub 2014 Nov 1.

PMID:
25366975
8.

A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra.

Xu H, Freitas MA.

BMC Bioinformatics. 2010 Aug 23;11:436. doi: 10.1186/1471-2105-11-436.

9.

Enhanced peptide quantification using spectral count clustering and cluster abundance.

Lee S, Kwon MS, Lee HJ, Paik YK, Tang H, Lee JK, Park T.

BMC Bioinformatics. 2011 Oct 28;12:423. doi: 10.1186/1471-2105-12-423.

10.

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ, Metz TO, Anderson GA, Smith RD.

BMC Bioinformatics. 2013 Feb 12;14:49. doi: 10.1186/1471-2105-14-49.

11.

Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID).

Kelstrup CD, Frese C, Heck AJ, Olsen JV, Nielsen ML.

Mol Cell Proteomics. 2014 Aug;13(8):1914-24. doi: 10.1074/mcp.O113.035915. Epub 2014 Jun 3.

12.

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29.

13.

Implementation and application of a versatile clustering tool for tandem mass spectrometry data.

Flikka K, Meukens J, Helsens K, Vandekerckhove J, Eidhammer I, Gevaert K, Martens L.

Proteomics. 2007 Sep;7(18):3245-58.

PMID:
17708593
14.

A spectral clustering approach to MS/MS identification of post-translational modifications.

Falkner JA, Falkner JW, Yocum AK, Andrews PC.

J Proteome Res. 2008 Nov;7(11):4614-22. doi: 10.1021/pr800226w. Epub 2008 Sep 19.

PMID:
18800783
15.

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling.

Chapman JD, Goodlett DR, Masselon CD.

Mass Spectrom Rev. 2014 Nov-Dec;33(6):452-70. doi: 10.1002/mas.21400. Epub 2013 Nov 26. Review.

PMID:
24281846
16.

Code developments to improve the efficiency of automated MS/MS spectra interpretation.

Sadygov RG, Eng J, Durr E, Saraf A, McDonald H, MacCoss MJ, Yates JR 3rd.

J Proteome Res. 2002 May-Jun;1(3):211-5.

PMID:
12645897
17.

Postexperiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS.

Shin B, Jung HJ, Hyung SW, Kim H, Lee D, Lee C, Yu MH, Lee SW.

Mol Cell Proteomics. 2008 Jun;7(6):1124-34. doi: 10.1074/mcp.M700419-MCP200. Epub 2008 Feb 25.

18.

Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses.

Scherl A, Tsai YS, Shaffer SA, Goodlett DR.

Proteomics. 2008 Jul;8(14):2791-7. doi: 10.1002/pmic.200800045.

PMID:
18655048
19.

DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.

Petyuk VA, Mayampurath AM, Monroe ME, Polpitiya AD, Purvine SO, Anderson GA, Camp DG 2nd, Smith RD.

Mol Cell Proteomics. 2010 Mar;9(3):486-96. doi: 10.1074/mcp.M900217-MCP200. Epub 2009 Dec 17.

20.

MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

Victor KG, Murgai M, Lyons CE, Templeton TA, Moshnikov SA, Templeton DJ.

J Am Soc Mass Spectrom. 2010 Jan;21(1):80-7. doi: 10.1016/j.jasms.2009.09.007. Epub 2009 Sep 17.

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