Proteomics Core FacilityLinks and Tutorials

Bookshelf

This page lists a number of review articles that we found useful, related to concepts and practical applications of proteomic techniques. They are grouped by the following topics:

Proteomic workflows
Sample preparation
2D gel electrophoresis
LC-MS
Peptide fragmentation and sequencing
Phosphoproteomics
Other post-translational modifications
Intact proteins
Quantification
Targeted proteomics
Bioinformatics

 

Proteomic workflows

Proteomics by mass spectrometry: approaches, advances, and applications.
Yates JR, Ruse CI, Nakorchevsky A.
Annu Rev Biomed Eng. 2009;11:49-79.
http://www.ncbi.nlm.nih.gov/pubmed/19400705

Applying mass spectrometry-based proteomics to genetics, genomics and network biology.
Gstaiger M, Aebersold R.
Nat Rev Genet. 2009 Sep;10(9):617-27.
http://www.ncbi.nlm.nih.gov/pubmed/19687803

Mass spectrometry for proteomics.
Han X, Aslanian A, Yates JR 3rd.
Curr Opin Chem Biol. 2008 Oct;12(5):483-90.
http://www.ncbi.nlm.nih.gov/pubmed/18718552

Mass spectrometry and protein analysis.
Domon B, Aebersold R.
Science. 2006 Apr 14;312(5771):212-7.
http://www.ncbi.nlm.nih.gov/pubmed/16614208

 

Sample preparation

Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow.
Gundry RL, White MY, Murray CI, Kane LA, Fu Q, Stanley BA, Van Eyk JE.
Curr Protoc Mol Biol. 2009 Oct;Chapter 10:Unit10.25.
http://www.ncbi.nlm.nih.gov/pubmed/19816929

Trends in sample preparation for classical and second generation proteomics.
Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM.
J Chromatogr A. 2007 Jun 15;1153(1-2):235-58. Epub 2007 Jan 18.
http://www.ncbi.nlm.nih.gov/pubmed/17276441

 

2D gel electrophoresis

Difference gel electrophoresis.
Timms JF, Cramer R.
Proteomics. 2008 Dec;8(23-24):4886-97.
http://www.ncbi.nlm.nih.gov/pubmed/19003860

Difference gel electrophoresis.
Minden JS, Dowd SR, Meyer HE, Stühler K.
Electrophoresis. 2009 Jun;30 Suppl 1:S156-61.
http://www.ncbi.nlm.nih.gov/pubmed/19517495

 

LC-MS

Multidimensional LC separations in shotgun proteomics.
Motoyama A, Yates JR 3rd.
Anal Chem. 2008 Oct 1;80(19):7187-93
http://www.ncbi.nlm.nih.gov/pubmed/18826178

Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications.
Qian WJ, Jacobs JM, Liu T, Camp DG 2nd, Smith RD.
Mol Cell Proteomics. 2006 Oct;5(10):1727-44. Epub 2006 Aug 3.
http://www.ncbi.nlm.nih.gov/pubmed/16887931

 

Peptide fragmentation and sequencing

The ABC's (and XYZ's) of peptide sequencing.
Steen H, Mann M.
Nat Rev Mol Cell Biol. 2004 Sep;5(9):699-711
http://www.ncbi.nlm.nih.gov/pubmed/15340378

Collision-induced dissociation (CID) of peptides and proteins.
Wells JM, McLuckey SA.
Methods Enzymol. 2005;402:148-85.
http://www.ncbi.nlm.nih.gov/pubmed/16401509

Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.
Sadygov RG, Cociorva D, Yates JR 3rd.
Nat Methods. 2004 Dec;1(3):195-202
http://www.ncbi.nlm.nih.gov/pubmed/15789030

Protein identification by tandem mass spectrometry and sequence database searching.
Nesvizhskii AI.
Methods Mol Biol. 2007;367:87-119.
http://www.ncbi.nlm.nih.gov/pubmed/17185772

Collisions or electrons? Protein sequence analysis in the 21st century.
Coon JJ.
Anal Chem. 2009 May 1;81(9):3208-15.
http://www.ncbi.nlm.nih.gov/pubmed/19364119

 

Phosphoproteomics

Quantitative phosphoproteomics by mass spectrometry: past, present, and future.
Nita-Lazar A, Saito-Benz H, White FM.
Proteomics. 2008 Nov;8(21):4433-43.
http://www.ncbi.nlm.nih.gov/pubmed/18846511

Phosphopeptide fragmentation and analysis by mass spectrometry.
Boersema PJ, Mohammed S, Heck AJ.
J Mass Spectrom. 2009 Jun;44(6):861-78.
http://www.ncbi.nlm.nih.gov/pubmed/19504542

Phosphoproteomics for the masses.
Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ.
ACS Chem Biol. 2010 Jan 15;5(1):105-19.
http://www.ncbi.nlm.nih.gov/pubmed/20047291

Analytical strategies for phosphoproteomics.
Thingholm TE, Jensen ON, Larsen MR.
Proteomics. 2009 Mar;9(6):1451-68.
http://www.ncbi.nlm.nih.gov/pubmed/19235172

 

Other post-translational modifications

Interpreting the protein language using proteomics.
Jensen ON.
Nat Rev Mol Cell Biol. 2006 Jun;7(6):391-403.
http://www.ncbi.nlm.nih.gov/pubmed/16723975

Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques.
Zhao Y, Jensen ON.
Proteomics. 2009 Oct;9(20):4632-41.
http://www.ncbi.nlm.nih.gov/pubmed/19743430

Current approaches for global post-translational modification discovery and mass spectrometric analysis.
Hoffman MD, Sniatynski MJ, Kast J.
Anal Chim Acta. 2008 Oct 3;627(1):50-61. Epub 2008 Mar 22.
http://www.ncbi.nlm.nih.gov/pubmed/18790127

Proteomic analysis of post-translational modifications.
Mann M, Jensen ON.
Nat Biotechnol. 2003 Mar;21(3):255-61.
http://www.ncbi.nlm.nih.gov/pubmed/12610572

 

Intact proteins

Native mass spectrometry: a bridge between interactomics and structural biology.
Heck AJ.
Nat Methods. 2008 Nov;5(11):927-33
http://www.ncbi.nlm.nih.gov/pubmed/18974734

Protein complexes in the gas phase: technology for structural genomics and proteomics.
Benesch JL, Ruotolo BT, Simmons DA, Robinson CV.
Chem Rev. 2007 Aug;107(8):3544-67. Epub 2007 Jul 25
http://www.ncbi.nlm.nih.gov/pubmed/17649985

 

Quantification

Peptide and protein quantification: a map of the minefield.
Vaudel M, Sickmann A, Martens L.
Proteomics. 2010 Feb;10(4):650-70.
http://www.ncbi.nlm.nih.gov/pubmed/19953549

Mass spectrometry-based proteomics turns quantitative.
Ong SE, Mann M.
Nat Chem Biol. 2005 Oct;1(5):252-62.
http://www.ncbi.nlm.nih.gov/pubmed/16408053

Functional and quantitative proteomics using SILAC.
Mann M.
Nat Rev Mol Cell Biol. 2006 Dec;7(12):952-8.
http://www.ncbi.nlm.nih.gov/pubmed/17139335

A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC).
Ong SE, Mann M.
Nat Protoc. 2006;1(6):2650-60.
http://www.ncbi.nlm.nih.gov/pubmed/17406521

Quantitative mass spectrometry in proteomics: a critical review.
Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B.
Anal Bioanal Chem. 2007 Oct;389(4):1017-31. Epub 2007 Aug 1.
http://www.ncbi.nlm.nih.gov/pubmed/17668192

Current trends in quantitative proteomics.
Elliott MH, Smith DS, Parker CE, Borchers C.
J Mass Spectrom. 2009 Dec;44(12):1637-60.
http://www.ncbi.nlm.nih.gov/pubmed/19957301

 

Targeted proteomics

Selected reaction monitoring for quantitative proteomics: a tutorial.
Lange V, Picotti P, Domon B, Aebersold R.
Mol Syst Biol. 2008;4:222. Epub 2008 Oct 14.
http://www.ncbi.nlm.nih.gov/pubmed/18854821

Perspectives of targeted mass spectrometry for protein biomarker verification.
Hüttenhain R, Malmström J, Picotti P, Aebersold R.
Curr Opin Chem Biol. 2009 Dec;13(5-6):518-25. Epub 2009 Oct 7.
http://www.ncbi.nlm.nih.gov/pubmed/19818677

 

Bioinformatics

Bioinformatics analysis of mass spectrometry-based proteomics data sets.
Kumar C, Mann M.
FEBS Lett. 2009 Jun 5;583(11):1703-12. Epub 2009 Mar 21.
http://www.ncbi.nlm.nih.gov/pubmed/19306877

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.
Deutsch EW, Lam H, Aebersold R.
Physiol Genomics. 2008 Mar 14;33(1):18-25. Epub 2008 Jan 22.
http://www.ncbi.nlm.nih.gov/pubmed/18212004

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases.
Käll L, Storey JD, MacCoss MJ, Noble WS.
J Proteome Res. 2008 Jan;7(1):29-34. Epub 2007 Dec 8.
http://www.ncbi.nlm.nih.gov/pubmed/18067246

Analysis and validation of proteomic data generated by tandem mass spectrometry.
Nesvizhskii AI, Vitek O, Aebersold R.
Nat Methods. 2007 Oct;4(10):787-97.
http://www.ncbi.nlm.nih.gov/pubmed/17901868