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Introduction to Proteomics
Introduction to Statistical Analysis in Scaffold
Ascore - Gygi Lab
File Compatibility Matrix
Loading Search Engine Results into Scaffold
Scaffold User Guide
Scaffold Batch User Guide
Scaffold Q+/Q+S User Guide
Scaffold Batch Q+/Q+S User Guide
Scaffold perSPECtives User Guide
Scaffold PTM User Guide
ABRF sPRG Study Finds Field is Precise but Still Struggles with Accuracy in Quantitative Proteomics (2014)
Precursor Intensity Quantitation in Scaffold, Q+ and Q+S (2015)
Scaffold Suite: Available Reports (2014)
Scaffold Suite File Compatibility Matrix
Configuring Proteome Discoverer 2.0 (2015)
Configuring Proteome Discoverer for optimal performance in Scaffold 4(2015)
Scaffold Protein Grouping and Clustering
Scaffold 4 Features Guide
Terminology Comparison between Scaffold4 and Scaffold3 Display Options (2013)
Loading PLGS 3.0 data into Scaffold 4
Explanation of Scaffold3 Display Options
Loading PLGS Data into Scaffold 3
Scaffold Support for Protein Lynx Data
Grouping Algorithm Explained: Understanding the Intricacies of Protein Grouping in Scaffold
Customizing GO Annotations
Normalizing Spectral Counts in Scaffold
High Mass Accuracy Scoring
Kernel Density Function for Protein Abundance
The Randomized Permutation Test
Normalization in Q+
Treatment of Missing Values in Q+
Quantification Setup in Scaffold Q+ 3.4.0
Ascore Probability Description
ScaffoldBatch Processing: New Features for Sage-N's Processor
Improving Quantitation in Scaffold PTM
(ASMS 2015, User Group)
Analysis of GeLCMS Data in Scaffold
(ASMS 2015, User Group)
The New Quantify View in Scaffold
(ASMS 2015, User Group)
A Complete Framework for Metabolomics
(ASMS 2015, User Group)
Improving Peptide Probability Modeling (LFDR Scoring Algorithm)
(ASMS 2013, User Group)
FDR Thresholding and Clustering
(ASMS 2013, User Group)
Scaffold 4 New Features
(ASMS 2013, User Group)
Advancing Statistical Analysis of Multiplexed MS/MS Quantitative Data with Scaffold Q+
Scaffold PTM 2.0
(User's Group 2012)
Reporting Protein Identifications from MS/MS Results
Organizing MS/MS Proteomic Data for Publication with Scaffold
Interpreting MS/MS Proteomics Results
(NPC Progress Meeting, 2006)
X! Tandem Explained
Improving Peptide and Protein Identification Rates Using a Novel Semi-Supervised Approach in Scaffold (2013)
Protein Cluster Identification and Quantitation with Scaffold (2013)
Using MS MS Total Ion Current (TIC) Quantification in Scaffold 3 Software - Comparison to Spectral Counting (2011)
Probabilistically Assigning Sites of Protein Modification with Scaffold PTM (2011)
Testing for Differences Between Complex Samples in Proteomics Datasets (2009)
Quantitation Across Multiple iTRAQ Samples Using Scaffold Q+ (2009)
Improving Sensitivity by Combining MS MS Results (2007)
The Effect of Data Analysis Choices on the Number of Proteins Identified in MS MS Proteomics Experiments (2006)
Improving Computer Interpretation of Linear Ion Trap Data Using Scaffold (2006)
Identifying Peptides the Way Experts Do: A Scientist-Driven Scoring System for Improving MS MS Peptide Identification Confidence (2006)
Use of Multiple Peptide Identification Programs to Increase Peptide and Protein Identifications in Human Whole Saliva (2006)
Scaffold: A Program to Probabilistically Combine Results from Multiple MS MS Database Search Engines (2005)
"Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly."
Nat. Cell Biol.
Horton ER, Byron A, Askari JA, Ng DH, Millon-Frémillon A, Robertson J, Koper EJ, Paul NR, Warwood S, Knight D, Humphries JD, Humphries MJ.
"Genetic background is a key determinant of glomerular extracellular matrix composition and organization"
J. Am. Soc. Nephrol. (2015)
J. Am. Soc. Nephrol. (2
015), alternative link
Randles MJ, Woolf AS, Huang JL, Byron A, Humphries JD, Price KL, Kolatsi-Joannou M, Collinson S, Denny T, Knight D, Mironov A, Starborg T, Korstanje R, Humphries MJ, Long DA, Lennon R.
"Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling"
Nat. Commun. (2015) 6: 6265
Nat. Commun. (2015) 6: 6265, alternative link
Robertson J, Jacquemet G, Byron A, Jones MC, Warwood S, Selley JN, Knight D, Humphries JD, Humphries MJ.
"A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting"
Nat. Commun. (2015) 6: 6135.
Nat. Commun. (2015) 6: 6135, alternative link
Byron A, Askari JA, Humphries JD, Jacquemet G, Koper EJ, Warwood S, Choi CK, Stroud MJ, Chen CS, Knight D, Humphries MJ.
"Microtubule-dependent modulation of adhesion complex composition"
PLoS One (2014) 9(12): e115213.
PLoS One (2014) 9(12): e115213
, alternative link
Ng DH, Humphries JD, Byron A, Millon-Frémillon A, Humphries MJ.
"Global analysis reveals the complexity of the human glomerular extracellular matrix"
J. Am. Soc. Nephrol. (2014) 25(5): 939-51.
J. Am. Soc. Nephrol. (2014) 25(5): 939-51, alternative link
Lennon R, Byron A, Humphries JD, Randles MJ, Carisey A, Murphy S, Knight D, Brenchley PE, Zent R, Humphries MJ.
"Comparison of Fractionation Strategies Post-Enrichment by Titania used in the Study of the Phosphoproteome of a Green Alga"
ABRF 2014 Waters Award Poster
Naldrett M.J., Marsh E.L., Alvarez S. and Evans B.S.
“Circulating pEGFR is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer”
Clinical Cancer Research. 2014, 20(24):6346-56
Katsila T, Juliachs M, Gregori J, Macarulla T, Villarreal L,, Bardelli A, Torrance C, Elez, E, Tabernero J and Villanueva J*.
“Enhancing the Biological Relevance of Secretome-based Proteomics by Linking Tumor Cell Proliferation and Protein Secretion”
J Proteome Research. 2014. 13 (8), 3706–3721
Gregori J, Méndez O, Katsila T, Pujals M, Salvans C, Villarreal L, Arribas J, Tabernero J, Sánchez A, Villanueva J*.
"Linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake (Crotalus adamanteus)"
Journal of Proteomics Volume 96
, 16 January 2014, Pages 145–158
Margres M.J., McGivern J.J., Wray K.P., Seavy M.,Calvin K. and Rokyta D.R.
"Rac1 is deactivated at integrin activation sites through an IQGAP1-filamin-A-RacGAP1 pathway"
J. Cell Sci. (2013) 126(18): 4121-35.
J. Cell Sci. (2013) 126(18): 4121-35, alternative link
Jacquemet G, Morgan MR, Byron A, Humphries JD, Choi CK, Chen CS, Caswell PT, Humphries MJ.
“An effect size filter improves the reproducibility in spectral counting-based comparative proteomics”
Journal of Proteomics, June 2013, S1874-3919(13)
Gregori J, Villarreal L, Sánchez A, Baselga J, Villanueva J*.
"Proteomic anatomy of human skin"
Journal of Proteomics, Volume 84, 12 June 2013, Pages 190–200
Leann M. Mikesha, Lavakumar Reddy Aramadhakaa, Christopher Moskalukb, Paola Zigrinoc, Cornelia Mauchc, Jay W. Fox
“Unconventional secretion is a major contributor of cancer cell line secretomes”
Molecular & Cellular Proteomics. 2013, 12(5):1046-60
Villarreal L, Méndez O, Salvans C, Gregori J, Baselga J, Villanueva J*.
"Bovine milk proteome: Quantitative changes in normal milk exosomes, milk fat globule membranes and whey proteomes resulting from Staphylococcus aureus mastitis."
Journal of Proteomics 82: 141-154, 2013
Reinhardt, Timothy A., Randy E. Sacco, Brian J. Nonnecke, and John D. Lippolis.
"Investigating the molecular mechanisms of the interactions between Lactobacillus reuteri strains and intestinal mucus."
Thesis submitted for the degree of Doctor of Philosophy, September 2012
Faye Jeffers, University of East Anglia, Institute of Food Research, Norwich, UK
"Batch effects correction improves the sensitivity of significance tests in spectral counting-based comparative discovery proteomics”
Journal of Proteomics 75, no. 13: 3938-51, 2012
Gregori J, Villarreal L, Méndez O, Sánchez A, Baselga J, Villanueva J*.
"Bovine milk exosome proteome."
Journal of Proteomics 75, no. 5: 1486-1492, 2012
Reinhardt, Timothy A., John D. Lippolis, Brian J. Nonnecke, and Randy E. Sacco.
"Shotgun proteomics-based clinical testing for diagnosis and classification of amyloidosis."
J Mass Spectrom. 2013 Oct;48(10) 1078-1127
Theis JD, Dasari S, Vrana JA, Kurtin PJ, and Dogan A
"Proteomics of human plasma: A critical comparison of analytical workflows in terms of effort, throughput and outcome."
EuPA Open Proteomics. 2013.08.001; (1) 8-16
Dayona L and Kussmanna M
"Comparative proteomic analysis of supportive and unsupportive extracellular matrix substrates for human embryonic stem cell maintenance."
J. Biol. Chem. 2013 May: (288) 18716-18731
J. Biol. Chem. 2013 May: (288) 18716-18731
Soteriou D, Iskender B, Byron A, Humphries JD, Borg-Bartolo S, Haddock MC, Baxter MA, Knight D, Humphries MJ, Kimber SJ
"Proteomic analysis of extracellular matrix from the hepatic stellate cell line LX-2 identifies CYR61 and Wnt-5a as novel constituents of fibrotic liver."
J.Proteome Res. 2012 Aug 3;11(8):4052-4064
J.Proteome Res. 2012 Aug 3;11(8):4052-4064, alternative link
Rashid ST, Humphries JD, Byron A, Dhar A, Askari JA, Selley JN, Knight D, Goldin RD, Thursz M, Humphries MJ
"Proteomic analysis of α4β1 integrin adhesion complexes reveals α-subunit-dependent protein recruitment"
Proteomics. 2012 Jul;12(13):2107-14. doi: 10.1002/pmic.201100487
Proteomics. 2012 Jul;12(13):2107-14. doi: 10.1002/pmic.201100487, alternative link
Byron A, Humphries JD, Bass MD, Knight D, Humphries MJ
"Effects of Space Flight on the Expression of Liver Proteins in the Mouse"
J Proteomics Bioinform (2012) 5: 256-261. doi 10.4172/jpb.1000246
Gridley DS, Pecaut MJ, Green LM, Herrmann EC, Bianski B, Slater JM, Stodieck LS, Ferguson VL and Sandberg LB
"A Face in the Crowd: Recognizing Peptides Through Database Search"
Molecular & Cellular Proteomics. 2011 Aug 10: R111.009522
Jimmy K Eng, Brian C Searle, Karl R Clauser and David L Tabb.
"Proteomic Analysis of Integrin Adhesion Complexes"
Sci. Signal., 5 April 2011, Vol. 4, Issue 167, p. pt2
Sci. Signal., 5 April 2011, Vol. 4, Issue 167, p. pt2, alternative link
Byron A, Humphries JD, Bass MD, Knight D, Humphries MJ.
"Protein identification using Sorcerer 2 and SEQUEST"
Curr Protocol Bioinformatics. 2009 Dec;13(13.3)
Martinez Lundgren and Han Wright.
“Proteomic Analysis of Integrin-Associated Complexes Identifies RCC2 as a Dual Regulator Rac1 Arf6”
Sci Signal. 2009 Sept;2(87):ra51
Jonathan D. Humphries, Adam Byron, Mark D. Bass, Sue E. Craig, John W. Pinney, David Knight, and Martin Humphries
“Extensive fractionation and identification of proteins within nasal lavage fluids from allergic rhinitis and asthmatic chronic rhinosinusitis patients”
J Sep Sci. 2009 Jan;32(1):44-56
Benson LM, Mason CJ, Friedman O, Kita H, Bergen HR 3rd, Plager DA.
“Pathway-based biomarker search by high-throughput proteomics profiling of secretomes"
J Proteome Research. 2009. 8(3):1489-503
Lawlor K, Nazarian A, Lacomis L, Tempst P, Villanueva J*.
Temporal Quantitative Proteomics by iTRAQ 2D-LC-MS/MS and Corresponding mRNA Expression Analysis Identify Post-Transcriptional Modulation of Actin-Cytoskeleton Regulators During TGF-β-Induced Epithelial-Mesenchymal Transition”
J. Proteome Res., 2009, 8 (1), pp 35–47
Venkateshwar G. Keshamouni, Pratik Jagtap, George Michailidis, John R. Strahler, Rork Kuick, Ajaya Kumar Reka, Panagiotis Papoulias, Rashmi Krishnapuram, Anjaiah Srirangam, Theodore J. Standiford, Philip C. Andrews and Gilbert S. Omenn
“Chicken egg yolk cytoplasmic proteome, mined via combinatorial peptide ligand libraries”
Journal of Chromatography A Volume 1216, Issue 8, 20 February 2009, Pages 1241-1252
Farinazzo A, Restuccia U, Bachi A, Guerrier L, Fortis F, Boschetti E, Fasoli E, Citterio A, Righetti PG.
“Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes”
Nucleic Acids Research, 2008, Vol. 36, No. 22 6959–6976
Ken Sin Lo, Sylvie Bourassa
Michael J. Hendzel
Valina L. Dawson
Ted M. Dawson and Guy G. Poirier.
“Combining Results from Lectin Affinity Chromatography and Glycocapture Approaches Substantially Improves the Coverage of the Glycoproteome”
Mol Cell Proteomics 2008: 287–301
Claudia A. McDonald, Jane Y. Yang, Vinita Marathe, Ten-Yang Yen, and Bruce A. Macher
“Proteomic analysis of membrane rafts of melanoma cells identifies protein patterns characteristic of the tumor progression stage”
Cell Biology Volume 8 Issue 22, Oct 2008 4733 – 4747
Frédérique Baruthio, Manfredo Quadroni, Curzio Rüegg, Agnese Mariotti, Dr.
“Alterations in protein expression associated with the development of mealiness in peaches”
Journal of Horticultural Science & Biotechnology, 2008 83 (1) 85–93
D. M. Obenland,W. H.Vensel and W. J. Hurkman
“Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile”
Journal of Proteome Research 2008, 7, 1027–1035
Sunia A. Trauger, Ewa Kalisak, Jaroslaw Kalisiak, Hirotoshi Morita, Michael V. Weinberg, Angeli Lal Menon, Farris L. Poole II, Michael W. W. Adams, and Gary Siuzdak
“Identification of Fructose-1,6-bisphosphate aldolase cytosolic class I as an NMH7 MADS domain associated protein”
Biochemical and Biophysical Research Communications Volume 376, Issue 4, 28 November 2008, 700-705
Julio Páez-Valencia, Pedro Valencia-Mayoral, Concepción Sánchez-Gómez, Alejandra Contreras-Ramos, Ismael Hernández-Lucas, Eleazar Martínez-Barajas and Alicia Gamboa-deBuen
“Identification of Differentially Expressed Proteins in the Cervical Mucosa of HIV-1-Resistant Sex Workers”
J. Proteome Research 2008, 7 (10), pp 4446–4454
Adam Burgener, Julie Boutilier, Charles Wachihi, Joshua Kimani, Michael Carpenter, Garrett Westmacott, Keding Cheng, Terry B. Ball and Francis Plummer
“Proteomic Analysis of Rat Striatal Synaptosomes during Acrylamide Intoxication at a Low Dose Rate”
Toxicological Sciences 100(1), August, 2007 156–167
David S. Barber, Stanley Stevens, and Richard M. LoPachin
"Intracellular Trafficking of a Polymorphism in the Carboxyl Terminus of the Alpha Subunit of the Human Epithelial Sodium Channel is Modulated by Casein Kinase”
J Am J Physiol Renal Physiol, 2007
Yan, W, Spruce L, Rosenblatt M, Kleyman, T, Rubenstein R,
"Proteomic analysis of cervical-vaginal fluid: identification of novel biomarkers for detection of intra-amniotic infection"
J Proteome Res. 2007 Jan;6(1):89-96
Gravett MG, Thomas A, Schneider KA, Reddy AP, Dasari S, Jacob T, Lu X, Rodland M, Pereira L, Sadowsky DW, Roberts CT Jr, Novy MJ, Nagalla SR.
"Global Assessment of Regulation of Phosphorylation of Insulin Receptor Substrate-1 by Insulin In Vivo in Human Muscle"
J Diabetes, 56:1508-1516, 2007 Vol. 7, No.3
Yi Z, Langlais P, De Filippis E, Luo M, Flynn C, Schroeder S, Weintraub S, Mapes R, Mandarino L
"Proteomic Analysis of human amniotic fluid"
Molecular & Cellular Proteomics 6:1406-1415, 2007
Chan-Kyung J. Cho, Shannon J. Shan, Elizabeth J. Winsor and Eleftherios P. Diamandis
"Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis"
Molecular & Cellular Proteomics 6:1198-1214, 2007
Benschop J, Mohammed S, O'Flaherty M, Heck A, Slijper M, Menk F
"Pfnek3 functions as an atypical MAPKK in Plasmodium falciparum "
Biochemical and Biophysical Research Communications Volume 361, Issue 2, 21 September 2007, Pages 439-444
Huiyu Low, Yu Min Lye and Tiow-Suan Sim
"Proteomics Evaluation of Chemically Cleavable Activity-based Probes"
Molecular Cellular Proteomics 6 (10), 1761-70 (01 Oct 2007)
Fonovic M, Verhelst SH, Sorum MT, Bogyo M.
"Proteomic analysis of ovomucoid hypersensitivity in mice by two-dimensional difference gel electrophoresis (2D-DIGE)"
Food and Chemical Toxicology Volume 45, Issue 12, December 2007, Pages 2372-2380
D.J. Hobson, P. Rupa, G.J. Diaz 1, H. Zhang, M. Yang, Y. Mine, P.V. Turner and G.M. Kirby
"Structure-Toxicity Analysis of Type-2 Alkenes: In Vitro Neurotoxicity"
Toxicol. Sci., Jan 2007; 95: 136 - 146.
Richard M. LoPachin, David S. Barber, Brian C. Geohagen, Terrence Gavin, Deke He, and Soma Das
"High copper selectively alters lipid metabolism and cell cycle machinery in the mouse model of Wilson disease"
J. Biol. Chem., Jan 2007; 10.1074/jbc.M607496200
Dominik Huster, Tina D. Purnat, Jason L. Burkhead, Martina Ralle, Oliver Fiehn, Franziska Stuckert, N. Erik Olson, Daniel Teupser, and Svetlana Lutsenko
"Tandem affinity purification of functional TAP-tagged proteins from human cells"
Nat. Protocols 2 (5), 1145-51 (May 2007)
Juraj Gregan, Christian G Riedel, Mark Petronczki, Lubos Cipak, Cornelia Rumpf, Ina Poser, Frank Buchholz, Karl Mechtler & Kim Nasmyth
"Molecular Cloning and Expression of a cDNA Encoding a Coccidioides posadasii Cu,Zn Superoxide Dismutase Identified by Proteomic Analysis of the Coccidioidal T27K Vaccine"
Annals of the New York Academy of Sciences 1111 (1), 181-97
Lunetta JM, Simmons KA, Johnson SM, Pappagianis D.
"Proteomic analysis of conditioned media from three breast cancer cell lines: A mine for biomarkers and therapeutic targets"
Molecular & Cellular Proteomics 6:1997-2011, 2007.
Vathany Kulasingam and Eleftherios Diamandis
"Endogenous phosphotyrosine signaling in zebrafish embryos"
Molecular Cellular Proteomics, M600482-MCP200 (14 Aug 2007)
Simone M. Lemeer, Rob Ruijtenbeek, Martijn W. H. Pinkse, Chris Jopling, Albert J. R. Heck, Jeroen den Hertog, and Monique Slijper
"Characterization of the human skeletal muscle proteome by one-dimensional Gel electrophoresis and HPLC-ESI-MS/MS"
Molecular Cellular Proteomics, M700304-MCP200 (01 Oct 2007)
Kurt Højlund, Zhengping Yi, Hyonson Hwang, Benjamin Bowen, Natalie Lefort, Charles R. Flynn, Paul Langlais, Susan T. Weintraub, and Lawrence J. Mandarino
"Suction blister fluid as potential body fluid for biomarker proteins"
Proteomics, 7(20) 3638-3650
Jeroen Kool, Léon Reubsaet, Feikje Wesseldijk, Raquel T. Maravilha, Martijn W. Pinkse, Clive S. D'Santos, Jacobus J. van Hilten, Freek J. Zijlstra, Albert J. R. Heck
"Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin"
Molecular Vision 2007; 13:2058-2065
David O. Zamora, Michael Riviere, Dongseok Choi, Yuzhen Pan, Stephen R. Planck, James T. Rosenbaum, Larry L. David, Justine R. Smith
"Cannabinoid WIN 55,212-2 Regulates TRPV1 Phosphorylation in Sensory Neurons"
J Bio Chem VOL. 281, NO. 43, pp. 32879–32890, October 27, 2006
Nathaniel A. Jeske, Amol M. Patwardhan, Nikita Gamper, Theodore J. Price, Armen N. Akopian, and Kenneth M. Hargreaves
"Analysis of the cGMP/cAMP Interactome Using a Chemical Proteomics Approach in Mammalian Heart Tissue Validates Sphingosine Kinase Type 1-interacting Protein as Genuine and Highly Abundant AKAP"
J Proteome Res 2006 5, 1435-1447
Scholten A, Poh, MK, van Veen, T, van Breukelen B, Vos M, Heck A
"The Anti-HIV-1 Editing Enzyme APOBEC3G Binds HIV-1 RNA and Messenger RNAs That Shuttle between Polysomes and Stress Granules "
J. Biol. Chem., Sep 2006; 281: 29105 - 29119.
Susan L. Kozak, Mariana Marin, Kristine M. Rose, Cory Bystrom, and David Kabat
"Disease State Differentiation and Identification of Tuberculosis Biomarkers via Native Antigen Array Profiling"
Mol. Cell. Proteomics, Nov 2006; 5: 2102 - 2113.
Todd M. Greco, Roberto Hodara, Ioannis Parastatidis, Harry F. G. Heijnen, Michelle K. Dennehy, Daniel C. Liebler, and Harry Ischiropoulos
"Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells"
PNAS, May 2006; 103: 7420 - 7425.
Mark J. Sartain, Richard A. Slayden, Krishna K. Singh, Suman Laal, and John T. Belisle
"Plasmodium falciparum AMA1 binds a rhoptry neck protein homologous to TgRON4, a component of the moving junction in Toxoplasma gondii."
Eukaryot Cell. 2006 Jul;5(7):1169-73.
Artigues A, Iriarte A, Martinez-Carrion M.
"Identification of Hsc70 binding sites in mitochondrial aspartate aminotransferase."
Arch Biochem Biophys. 2006 Jun 1;450(1):30-8
Alexander DL, Arastu-Kapur S, Dubremetz JF, Boothroyd JC.
"Lumbar Cerebrospinal Fluid Proteome in Multiple Sclerosis: Characterization by Ultrafiltration, Liquid Chromatography, and Mass Spectrometry"
J. Proteome Res.; 2006; 5(7) pp 1647 - 1657
Jean-Paul Noben, Debora Dumont, Natalia Kwasnikowska, Peter Verhaert, Veerle Somers, Raymond Hupperts, Piet Stinissen, and Johan Robben
"Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?"
J Proteome Res. 2006 Oct;5(10):2554-66
Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL.
"Identification of the moving junction complex of Toxoplasma gondii: a collaboration between distinct secretory organelles."
PLoS Pathog. 2005 Oct;1(2):e17. Epub 2005 Oct 21
Alexander DL, Mital J, Ward GE, Bradley P, Boothroyd JC.
Links & Other Resources
Search Engines and Other Programs
: SEQUEST is the original, and still one of the leading, programs that correlate uninterpreted MS/MS spectra of peptides with the amino acid sequences from protein databases. If you want to understand what SEQUEST is telling you, look at the interactive Sequest Browser summary page. SEQUEST is the search engine sold by Thermo Finnigan with its mass spectrometers.
, a special hardware platform for running an optimized version of SEQUEST, is available from Sage N Research. DtaSelect is a program that organizes Sequest results. The Wildcat Toolbox from the Arizona Proteomics Consortium has various perl programs for further organizing Sequest, X! Tandem and FASTA files.
: Mascot is a widely used program that also uses mass spectrometry data to identify proteins from protein databases. Mascot has a extensive set of web help pages that includes a lot of information on protein identification by MS. You can use Mascot, in a limited way, on the web for free.
: X!Tandem is a very fast seach engine which searches for matches of MS/MS spectra to a protein database. X!Tandem is free to use on the web or to download. X!Tandem works in conjunction with thegpm.org and can take advantage of the information gleaned from previous searches. It has an option, PPP, which searches first only the peptides that have been found most frequently for each protein. This can speed searches up by a factor of 20.
: Spectrum Mill is the peptide search engine that Agilent sells with its mass spectrometers. Spectrum Mill implements a workflow for the MS experiment. First Spectrum Mill does an assessment of the quality of the spectra and only searches the worthwhile spectra. It also validates the spectra both automatically and visually.
ProteinLynx and IdentityE
: ProteinLynx is the peptide search engine that Waters Micromass sells with its mass spectrometers. ProteinLynx manages a workflow which passes spectra not identified in the first search to a second or third search. For example the first search might be unmodified proteins, the second proteins with modifications and the third de novo sequencing followed by BLAST.
de novo - Peaks
: Peaks takes MS/MS spectra files and does de novo sequencing to directly figure out what the amino acid sequence of the peptide is. Lutefisk and PepNovo are well regarded de novo sequencing programs that are available for free. De novo sequencing is also a part of Spectrum Mill and ProteinLynx and is also available from Thermo as denovoX.
Fragment Ion Calculator
: If you have a peptide's sequence of amino acids, and want to see what the y and b ions are, use the Fragment Ion Calculator or Ion Predictor. This is useful if you want to understand the peaks that are labeled by SEQUEST or one of the other search engines.
: The standard MS/MS experiment starts by digesting the proteins into peptides with an enzyme such as trypsin. To see what peptides will result from digesting a protein, use the Protein Digestor or the equivalent here. You can download a similar program, Paws.
: In top down proteomics, an alternative way of gaining insight into a proteome, whole proteins are run through a mass spectrometer. ProSightPTM is the only software available for top down protein identification and characterization.
: A proteomics experiment involves much more than just mass spectrometry. There are also numerous steps of sample preparation, enrichment and/or depletion, separation and/or pooling. In additon as you can see above, there are a number of software processing steps. Laboratory information management systems (LIMS) can track all these operations. Proteus from Genologics is a LIMS oriented toward proteomics and mass spectrometry.
: This tool computes the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot proteins or for a sequence of amino acids. You can use this to check that the identified protein is consistent with its position on a 2D PAGE gel. Remember that real proteins in samples are often modified in ways that change pI and Mw from these theoretical values.
: The Association of Biological Resource Facilities (ABRF) discussion forum deals with biological techniques and proteomics methodology.
: Questions and answers on bioinformatics, computational genomics and systems biology.
Science Advisory Board
: The Science Advisory Board hosts an active list with discussing a wide variety of topics, including sections on proteomics, bioinformatics, software, and protocols.
: Chromatography Forum is a public discussion group where you can post questions, news, or messages of interest to chromatographers everywhere.
Proteomics Database Resources
Proteomic and Genomic Web Services
: Nucleic Acids Research also publishes an issue on web servers listing web tools that you can use such as BLAST, ESLpred, SDPpred, iMolTalk, ProMoST, and many, many others.
: Peptide atlas is a collection of MS/MS data that has been analyzed for peptide identification. The Open Proteomics Database, the Sashimi data repository, and Quartz also have proteomics mass spec data. The Global Proteome Machine (GPM) organization has a database for storing the results of searches by X!Tandem. The World 2D PAGE site lists 2D gels for many tissue samples.
HUPO - Human Proteomics Initiative
: This site's goal is to annotate all the known human proteins. This annotation will include function, domain structure, subcellular location, post-translational modifications, variants, and similarities to other proteins.
Human Genome Variation Society
: This site is your guide to databases that deal with mutations, polymorphisms, alleles, and SNPs. Some of these databases are oriented to specific human disorders. The Alternative Splicing Gallery shows how each gene is assembled into multiple proteins by splice variants.
ELM - Functional sites
: ELM predicts functional sites in eukaryotic proteins. This site has links to dozens of other sites that examine protein motifs and domains.
: MatchMiner is a set of tools that enables the user to translate between disparate ids for the same gene. It uses data from the UCSC, LocusLink, Unigene, OMIM, Affymetrix and Jackson data sources to determine how different ids relate. Supported id types include, gene symbols and names, IMAGE and FISH clones, GenBank accession numbers and UniGene cluster ids.
Tutorials and Information
Proteomics Interest Group at NIH
: At this site you can hear the experts speak (turn on your PC's speakers) and see the slides that they presented to the NIH proteome research community. The archive has past seminars, symposiums, tutorials and lectures.
Isotopes and Mass Spectrometry
: Atoms of carbon have isotopes of mass 12, 13, and 14 amu. Since proteins are made of carbon (and other atoms), the mass detected by the mass spectrometer for a protein depends upon the isotopes of the protein's atoms. You can learn what this means for protein identification in this IonSource tutorial. You can also develop a feel for isotopes by using Isotopica, Isotopident or an isotope calculator to work out examples.
: This site is an introduction to electrospray (ESI) by a company that makes electrosprays.
: Suppose you know what protein is in your sample. How can you measure how much of it there is? One method of measuring the amount of the protein uses a mass spectrometer and an internal standard. This tutorial from IonSource is aimed at mass spectrometrists. If you decide to do this, you can find peptides to use as internal standards at the Peptide Resource Page.
: Antibodies are the gold standard in protein identification. An antibody vendor, Chemicon, has made a very nice 36 page pdf "Introduction to Antibodies". To make sense of antibody discussions, remember that what you call a protein, they call an antigen. If you want to find an antibody for a particular purpose, the Antibody Resource Page is a good place to start looking.
Protein chemist tutorials
: This site has a number of tutorials on protein chemistry including purification, gels, antibodies, gels and modifications. It also has calculators for buffers and peptide characteristics.
: This site defines many of the common terms in proteomics. It is one of a number of interrelated glossaries and many of the terms are linked.
Little Encyclopedia of Mass Spectrometry
: Mass spectrometry has a sea of acronyms. To decode "ESI", "MALDI" and other mass spec terms, look at this cleverly constructed web page.
Language of HPLC
: If you don’t know what HPLC means, this is the web site to look it up. By the way, HPLC means High Pressure Liquid Chromatography and it is one standard way of separating peptides that are being fed into a mass spectrometer. Like other technologies, it has its special vocabulary.
: This site tries to help you if you are faced with “the daunting task” of acquiring the vocabulary of biochemistry. This site is not fancy, but if you are feeling daunted this might be what you need.
Molecular & Cellular Proteomics
: Most scientific journals are prohibitively expensive unless you work for an organization that subscribes to them for you. Not so with this journal which embraces open access. The papers are available free on-line from the day that they are accepted for publication. The "Papers in Press" have not yet formatted for publication.
: Proteome Science which has free on-line articles on proteomics research and methodology. There is about one new article per month. Other free journals are BMC BioTechnology and BMC BioInformatics and Nucleic Acids Research.
Proteomics at spectroscopyNOW
: The proteomics page of spectroscopyNOW has feature articles (you need to register), readable digests of scientific papers that have popular appeal, news about proteomics uses and the proteomics industry. Another page in this site is "BASE PEAK" claims to be "the web's leading mass spectrometry resource". SeparationsNOW is another web site by the same organization that also has a section on proteomics.
: This site is subtitled "The world of mass spectroscopy". It has news stories, interviews, product announcements and upcoming events related to mass spectrometry. About two or three new items are posted each week.
: The tagline for this web site is "Solutions for separation scientists". This magazine is targetted toward people who do chromatography, including HPLC.
: The buyer's guide for life scientists. If you want to buy a protein extraction kit and don't know where to look, this site will give you a lead.
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