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Results: 1 to 20 of 23

1.

A cross-platform toolkit for mass spectrometry and proteomics.

Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P.

Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377. No abstract available.

PMID:
23051804
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology.

Brusniak MY, Chu CS, Kusebauch U, Sartain MJ, Watts JD, Moritz RL.

Proteomics. 2012 Apr;12(8):1176-84. doi: 10.1002/pmic.201100571. Review.

PMID:
22577019
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

PASSEL: the PeptideAtlas SRMexperiment library.

Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Hüttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL.

Proteomics. 2012 Apr;12(8):1170-5. doi: 10.1002/pmic.201100515.

PMID:
22318887
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Proteomics Clin Appl. 2011 Dec;5(11-12):580-9. doi: 10.1002/prca.201100097.

PMID:
22213554
[PubMed - indexed for MEDLINE]
5.

TraML--a standard format for exchange of selected reaction monitoring transition lists.

Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY.

Mol Cell Proteomics. 2012 Apr;11(4):R111.015040. doi: 10.1074/mcp.R111.015040. Epub 2011 Dec 12.

PMID:
22159873
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

Proteomics. 2012 Jan;12(1):11-20. doi: 10.1002/pmic.201100562. Epub 2011 Dec 14.

PMID:
22069307
[PubMed - indexed for MEDLINE]
7.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

J Proteome Res. 2012 Feb 3;11(2):1412-9. doi: 10.1021/pr201071t. Epub 2011 Dec 8.

PMID:
22053864
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Mol Cell Proteomics. 2011 Dec;10(12):O111.015446. doi: 10.1074/mcp.O111.015446. Epub 2011 Nov 3.

PMID:
22052993
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L.

J Proteome Res. 2011 Nov 4;10(11):5260-3. doi: 10.1021/pr200664h. Epub 2011 Oct 13.

PMID:
21967198
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

mProphet: automated data processing and statistical validation for large-scale SRM experiments.

Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R.

Nat Methods. 2011 May;8(5):430-5. doi: 10.1038/nmeth.1584. Epub 2011 Mar 20.

PMID:
21423193
[PubMed - indexed for MEDLINE]
11.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.

Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R.

BMC Bioinformatics. 2011 Mar 18;12:78. doi: 10.1186/1471-2105-12-78.

PMID:
21414234
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage.

Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R.

Proteomics. 2011 Jan;11(1):154-8. doi: 10.1002/pmic.201000459. Epub 2010 Dec 6.

PMID:
21182202
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.

Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R.

Sci Signal. 2010 Dec 21;3(153):rs4. doi: 10.1126/scisignal.2001182.

PMID:
21177495
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry.

Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts JD, Aebersold R.

Mol Cell Proteomics. 2009 Aug;8(8):1934-46. doi: 10.1074/mcp.M800569-MCP200. Epub 2009 May 1.

PMID:
19411281
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.

PMID:
19087345
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform.

Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS, Vitek O, Zhang H, Aebersold R, Watts JD.

Clin Proteomics. 2008 Dec 1;4(3-4):105.

PMID:
20157627
[PubMed]
Free PMC Article
17.

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring.

Lange V, Malmström JA, Didion J, King NL, Johansson BP, Schäfer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY, Bühlmann P, Björck L, Domon B, Aebersold R.

Mol Cell Proteomics. 2008 Aug;7(8):1489-500. doi: 10.1074/mcp.M800032-MCP200. Epub 2008 Apr 13.

PMID:
18408245
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.

Mueller LN, Brusniak MY, Mani DR, Aebersold R.

J Proteome Res. 2008 Jan;7(1):51-61. doi: 10.1021/pr700758r. Epub 2008 Jan 4. Review.

PMID:
18173218
[PubMed - indexed for MEDLINE]
19.

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling.

Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M.

Proteomics. 2007 Oct;7(19):3470-80.

PMID:
17726677
[PubMed - indexed for MEDLINE]
20.

High-affinity interactions of ligands at recombinant guinea pig 5HT7 receptors.

Wilcox RE, Ragan JE, Pearlman RS, Brusniak MY, Eglen RM, Bonhaus DW, Tenner TE Jr, Miller JD.

J Comput Aided Mol Des. 2001 Oct;15(10):883-909.

PMID:
11918075
[PubMed - indexed for MEDLINE]

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