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SPS' DigestSpecial Issue "Missing articles for 2005" |
Comparison of different search engines using validated MS/MS test datasets
Kelly Boutilier, Mark Ross, Alexandre V. Podtelejnikov, Chris Orsi, Rod Taylor, Paul Taylor and Daniel Figeys
Analytica Chimica Acta (2005) 534(1): 11-20
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ
Proteomics (2005) 5(13): 3246-61
Plasma Proteome Database as a resource for proteomics research
Muthusamy B, Hanumanthu G, Suresh S, Rekha B, Srinivas D, Karthick L, Vrushabendra BM, Sharma S, Mishra G, Chatterjee P, Mangala KS, Shivashankar HN, Chandrika KN, Deshpande N, Suresh M, Kannabiran N, Niranjan V, Nalli A, Prasad TS, Arun KS, Reddy R, Chandran S, Jadhav T, Julie D, Mahesh M, John SL, Palvankar K, Sudhir D, Bala P, Rashmi NS, Vishnupriya G, Dhar K, Reshma S, Chaerkady R, Gandhi TK, Harsha HC, Mohan SS, Deshpande KS, Sarker M, Pandey A
Proteomics (2005) 5(13): 3531-6
Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies
Gulcicek EE, Colangelo CM, McMurray W, Stone K, Williams K, Wu T, Zhao H, Spratt H, Kurosky A, Wu B
Curr Protoc Bioinformatics (2005) Chapter 13: Unit 13.1
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis
Kapp EA, Schutz F, Connolly LM, Chakel JA, Meza JE, Miller CA, Fenyo D, Eng JK, Adkins JN, Omenn GS, Simpson RJ
Proteomics (2005) 5(13): 3475-90
Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds
Shadforth I, Dunkley T, Lilley K, Crowther D, Bessant C
Rapid Commun Mass Spectrom (2005) 19(22): 3363-8
Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative
Orchard S, Hermjakob H, Taylor C, Aebersold R, Apweiler R
Proteomics (2005) 5(18): 4651-2
Centralized data analysis of a large interlaboratory proteomics project: a feasibility study
Beer I, Barnea E, Admon A
Proteomics (2005) 5(13): 3491-6
Bioinformatics analysis for interactive proteomics
Chen Y, Xu D
Curr Protoc Protein Sci (2005) Chapter 25: Unit 25.1
A functional annotation of subproteomes in human plasma
Ping P, Vondriska TM, Creighton CJ, Gandhi TK, Yang Z, Menon R, Kwon MS, Cho SY, Drwal G, Kellmann M, Peri S, Suresh S, Gronborg M, Molina H, Chaerkady R, Rekha B, Shet AS, Gerszten RE, Wu H, Raftery M, Wasinger V, Schulz-Knappe P, Hanash SM, Paik YK, Hancock WS, States DJ, Omenn GS, Pandey A
Proteomics (2005) 5(13): 3506-19
Protein identification using TurboSEQUEST
Lundgren DH, Han DK, Eng JK
Curr Protoc Bioinformatics (2005) Chapter 13: Unit 13.3
PRIDE: the proteomics identifications database
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R
Proteomics (2005) 5(13): 3537-45
Error-tolerant EST database searches by tandem mass spectrometry and multiTag software
Liska AJ, Sunyaev S, Shilov IN, Schaeffer DA, Shevchenko A
Proteomics (2005) 5(16): 4118-22
ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer
Zhang N, Li XJ, Ye M, Pan S, Schwikowski B, Aebersold R
Proteomics (2005) 5(16): 4096-106
A statistical model for unwarping of 1-D electrophoresis gels
Glasbey C, Vali L, Gustafsson J
Electrophoresis (2005) 26(22): 4237-42
Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: multi-institution correlation of spectra and identification of biomarkers
Rai AJ, Stemmer PM, Zhang Z, Adam BL, Morgan WT, Caffrey RE, Podust VN, Patel M, Lim LY, Shipulina NV, Chan DW, Semmes OJ, Leung HC
Proteomics (2005) 5(13): 3467-74
Performance of the computer algorithm COMPLX for the detection of protein complexes in the mass spectra of simulated biological mixtures
Wong JW, Downard KM
J Mass Spectrom (2005) 40(9): 1187-96
Human Plasma PeptideAtlas
Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R
Proteomics (2005) 5(13): 3497-500
CD98, a novel marker of transient amplifying human keratinocytes
Lemaitre G, Gonnet F, Vaigot P, Gidrol X, Martin MT, Tortajada J, Waksman G
Proteomics (2005) 5(14): 3637-45
Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling
Nilsson P, Paavilainen L, Larsson K, Odling J, Sundberg M, Andersson AC, Kampf C, Persson A, Al-Khalili Szigyarto C, Ottosson J, Bjorling E, Hober S, Wernerus H, Wester K, Ponten F, Uhlen M
Proteomics (2005) 5(17): 4327-37
Proteomic identification of the TRAF6 regulation of vacuolar ATPase for osteoclast function
Ryu J, Kim H, Lee SK, Chang EJ, Kim HJ, Kim HH
Proteomics (2005) 5(16): 4152-60
The human plasma proteome: analysis of Chinese serum using shotgun strategy
He P, He HZ, Dai J, Wang Y, Sheng QH, Zhou LP, Zhang ZS, Sun YL, Liu F, Wang K, Zhang JS, Wang HX, Song ZM, Zhang HR, Zeng R, Zhao X
Proteomics (2005) 5(13): 3442-53
Identification of novel lysosomal matrix proteins by proteome analysis
Kollmann K, Mutenda KE, Balleininger M, Eckermann E, von Figura K, Schmidt B, Lubke T
Proteomics (2005) 5(15): 3966-78
A proteomic analysis of salivary glands of female Anopheles gambiae mosquito
Kalume DE, Okulate M, Zhong J, Reddy R, Suresh S, Deshpande N, Kumar N, Pandey A
Proteomics (2005) 5(14): 3765-77
Characterization of the human blood plasma proteome
Shen Y, Kim J, Strittmatter EF, Jacobs JM, Camp DG 2nd, Fang R, Tolie N, Moore RJ, Smith RD
Proteomics (2005) 5(15): 4034-45
Expression of fragile X mental retardation-1 gene with nuclear export signal mutation changes the expression profiling of mouse cerebella immortal neuronal cell
Hu L, Chen Y, Evers S, Shen Y
Proteomics (2005) 5(15): 3979-90
The proteome of maritime pine wood forming tissue
Gion JM, Lalanne C, Le Provost G, Ferry-Dumazet H, Paiva J, Chaumeil P, Frigerio JM, Brach J, Barre A, de Daruvar A, Claverol S, Bonneu M, Sommerer N, Negroni L, Plomion C
Proteomics (2005) 5(14): 3731-51
Subproteomic analysis of metal-interacting proteins in human B cells
Heiss K, Junkes C, Guerreiro N, Swamy M, Camacho-Carvajal MM, Schamel WW, Haidl ID, Wild D, Weltzien HU, Thierse HJ
Proteomics (2005) 5(14): 3614-22
Proteomic analysis of the excretory-secretory proteins of the Trichinella spiralis L1 larva, a nematode parasite of skeletal muscle
Robinson MW, Connolly B
Proteomics (2005) 5(17): 4525-32
Proteomics of human umbilical vein endothelial cells applied to etoposide-induced apoptosis
Bruneel A, Labas V, Mailloux A, Sharma S, Royer N, Vinh J, Pernet P, Vaubourdolle M, Baudin B
Proteomics (2005) 5(15): 3876-84
Reference maps of mouse serum acute-phase proteins: changes with LPS-induced inflammation and apolipoprotein A-I and A-II transgenes
Wait R, Chiesa G, Parolini C, Miller I, Begum S, Brambilla D, Galluccio L, Ballerio R, Eberini I, Gianazza E
Proteomics (2005) 5(16): 4245-53
Monocrotaline pyrrole targets proteins with and without cysteine residues in the cytosol and membranes of human pulmonary artery endothelial cells
Lame MW, Jones AD, Wilson DW, Segall HJ
Proteomics (2005) 5(17): 4398-413
Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM
Proteomics (2005) 5(13): 3226-45
Proteomic analysis of the porcine interphotoreceptor matrix
Hauck SM, Schoeffmann S, Deeg CA, Gloeckner CJ, Swiatek-de Lange M, Ueffing M
Proteomics (2005) 5(14): 3623-36
Proteome of endothelial cell-derived procoagulant microparticles
Banfi C, Brioschi M, Wait R, Begum S, Gianazza E, Pirillo A, Mussoni L, Tremoli E
Proteomics (2005) 5(17): 4443-55
Constitutive expression of heat shock protein p23 correlates with proneural territories in imaginal discs of Drosophila melanogaster
Alonso J, Rodriguez JM, Baena-Lopez LA, Alonso MT, Santaren JF
Proteomics (2005) 5(14): 3604-13
Proteomic analysis of the Gallus gallus embryo at stage-29 of development
Agudo Garcillan D, Gomez-Esquer F, Diaz-Gil G, Martinez-Arribas F, Delcan J, Schneider J, Palomar MA, Linares R
Proteomics (2005) 5(18): 4946-57
Plasma membrane-focused proteomics: dramatic changes in surface expression during the maturation of human dendritic cells
Watarai H, Hinohara A, Nagafune J, Nakayama T, Taniguchi M, Yamaguchi Y
Proteomics (2005) 5(15): 4001-11
Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display
Tammen H, Schulte I, Hess R, Menzel C, Kellmann M, Mohring T, Schulz-Knappe P
Proteomics (2005) 5(13): 3414-22
Plasma protein profiling: unique and stable features of individuals
Nelsestuen GL, Zhang Y, Martinez MB, Key NS, Jilma B, Verneris M, Sinaiko A, Kasthuri RS
Proteomics (2005) 5(15): 4012-24
Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project pilot phase
Berhane BT, Zong C, Liem DA, Huang A, Le S, Edmondson RD, Jones RC, Qiao X, Whitelegge JP, Ping P, Vondriska TM
Proteomics (2005) 5(13): 3520-30
Differential proteomic analysis of proteins in wheat spikes induced by Fusarium graminearum
Wang Y, Yang L, Xu H, Li Q, Ma Z, Chu C
Proteomics (2005) 5(17): 4496-503
A proteomic analysis of murine bone marrow and its response to ionizing radiation
Chen C, Lorimore SA, Evans CA, Whetton AD, Wright EG
Proteomics (2005) 5(16): 4254-63
Proteome analysis of embryo and endosperm from germinating tomato seeds
Sheoran IS, Olson DJ, Ross AR, Sawhney VK
Proteomics (2005) 5(14): 3752-64
Isolation and proteomic analysis [corrected] of cell wall-deficient Haematococcus pluvialis mutants
Wang SB, Chen F, Sommerfeld M, Hu Q
Proteomics (2005) 5(18): 4839-51
Differential proteomic analysis of proteins in wheat spikes induced by Fusarium graminearum
Wang Y, Yang L, Xu H, Li Q, Ma Z, Chu C
Proteomics (2005) 5(17): 4496-503
Proteome analysis of cortical neuronal cultures following cycloheximide, heat stress and MK801 preconditioning
Meloni BP, Van Dyk D, Cole R, Knuckey NW
Proteomics (2005) 5(18): 4743-53
Identification of Arabidopsis salt and osmotic stress responsive proteins using two-dimensional difference gel electrophoresis and mass spectrometry
Ndimba BK, Chivasa S, Simon WJ, Slabas AR
Proteomics (2005) 5(16): 4185-96
Proteomic analysis of organ-specific post-translational lysine-acetylation and -methylation in mice by use of anti-acetyllysine and -methyllysine mouse monoclonal antibodies
Iwabata H, Yoshida M, Komatsu Y
Proteomics (2005) 5(18): 4653-64
The accumulation of abundant soluble proteins changes early in the development of the primary roots of maize (Zea mays L.)
Hochholdinger F, Woll K, Guo L, Schnable PS
Proteomics (2005) 5(18): 4885-93
Proteome mapping of mature pollen of Arabidopsis thaliana
Holmes-Davis R, Tanaka CK, Vensel WH, Hurkman WJ, McCormick S
Proteomics (2005) 5(18): 4864-84
A reference map and identification of porcine testis proteins using 2-DE and MS
Huang SY, Lin JH, Chen YH, Chuang CK, Lin EC, Huang MC, Sunny Sun HF, Lee WC
Proteomics (2005) 5(16): 4205-12
Proteomic dataset of mouse aortic smooth muscle cells
Mayr U, Mayr M, Yin X, Begum S, Tarelli E, Wait R, Xu Q
Proteomics (2005) 5(17): 4546-57
MS characterization of multiple forms of alpha-amylase in human saliva
Hirtz C, Chevalier F, Centeno D, Rofidal V, Egea JC, Rossignol M, Sommerer N, de Periere DD
Proteomics (2005) 5(17): 4597-607
Proteomic analysis of neural differentiation of mouse embryonic stem cells
Wang D, Gao L
Proteomics (2005) 5(17): 4414-26
Proteomic analysis of rice embryo: an approach for investigating Galpha protein-regulated proteins
Komatsu S, Abbasi F, Kobori E, Fujisawa Y, Kato H, Iwasaki Y
Proteomics (2005) 5(15): 3932-41
Human serum and plasma proteomics
Musselman I, Speicher DW
Curr Protoc Protein Sci (2005) Chapter 24: Unit 24.1
Proteomic dataset of Sca-1+ progenitor cells
Yin X, Mayr M, Xiao Q, Mayr U, Tarelli E, Wait R, Wang W, Xu Q
Proteomics (2005) 5(17): 4533-45
Proteome analysis for the identification of in vivo estrogen-regulated proteins in bone
Pastorelli R, Carpi D, Airoldi L, Chiabrando C, Bagnati R, Fanelli R, Moverare S, Ohlsson C
Proteomics (2005) 5(18): 4936-45
Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12
Filen JJ, Nyman TA, Korhonen J, Goodlett DR, Lahesmaa R
Proteomics (2005) 5(18): 4719-32
Applying proteomics technology to platelet research
Garcia A, Watson SP, Dwek RA, Zitzmann N
Mass Spectrom Rev (2005) 24(6): 918-30
Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling
Nilsson P, Paavilainen L, Larsson K, Odling J, Sundberg M, Andersson AC, Kampf C, Persson A, Al-Khalili Szigyarto C, Ottosson J, Bjorling E, Hober S, Wernerus H, Wester K, Ponten F, Uhlen M
Proteomics (2005) 5(17): 4327-37
Fractionation and identification of proteins by 2-DE and MS: towards a proteomic analysis of Plasmodium falciparum
Gelhaus C, Fritsch J, Krause E, Leippe M
Proteomics (2005) 5(16): 4213-22
Proteomic analysis of rat laryngeal muscle following denervation
Li ZB, Lehar M, Samlan R, Flint PW
Proteomics (2005) 5(18): 4764-76
A quantitative proteomic analysis of growth factor-induced compositional changes in lipid rafts of human smooth muscle cells
MacLellan DL, Steen H, Adam RM, Garlick M, Zurakowski D, Gygi SP, Freeman MR, Solomon KR
Proteomics (2005) 5(18): 4733-42
The secretome of Pleurotus sapidus
Zorn H, Peters T, Nimtz M, Berger RG
Proteomics (2005) 5(18): 4832-8
Proteomic analysis of the response of human lung cells to uranium
Malard V, Prat O, Darrouzet E, Berenguer F, Sage N, Quemeneur E
Proteomics (2005) 5(17): 4568-80
A proteomics approach to identifying fish cell lines
Wagg SK, Lee LE
Proteomics (2005) 5(16): 4236-44
Proteome analysis of embryo and endosperm from germinating tomato seeds
Sheoran IS, Olson DJ, Ross AR, Sawhney VK
Proteomics (2005) 5(14): 3752-64
Wheat cultivar-specific proteins in grain revealed by 2-DE and their application to cultivar identification of flour
Yahata E, Maruyama-Funatsuki W, Nishio Z, Tabiki T, Takata K, Yamamoto Y, Tanida M, Saruyama H
Proteomics (2005) 5(15): 3942-53
Proteomic profiling of cholangiocarcinoma cell line treated with pomiferin from Derris malaccensis
Svasti J, Srisomsap C, Subhasitanont P, Keeratichamroen S, Chokchaichamnankit D, Ngiwsara L, Chimnoi N, Pisutjaroenpong S, Techasakul S, Chen ST
Proteomics (2005) 5(17): 4504-9
Characterization of pollen tube development in Pinus strobus (Eastern white pine) through proteomic analysis of differentially expressed proteins
Fernando DD
Proteomics (2005) 5(18): 4917-26
Pathogen elicitor-induced changes in the maize extracellular matrix proteome
Chivasa S, Simon WJ, Yu XL, Yalpani N, Slabas AR
Proteomics (2005) 5(18): 4894-904
Metabolic regulation at the tricarboxylic acid and glyoxylate cycles of the lignin-degrading basidiomycete Phanerochaete chrysosporium against exogenous addition of vanillin
Shimizu M, Yuda N, Nakamura T, Tanaka H, Wariishi H
Proteomics (2005) 5(15): 3919-31
1-DE MS and 2-D LC-MS analysis of the mouse bronchoalveolar lavage proteome
Guo Y, Ma SF, Grigoryev D, Van Eyk J, Garcia JG
Proteomics (2005) 5(17): 4608-24
Comparative study of protein and mRNA expression during osteoclastogenesis
Czupalla C, Mansukoski H, Pursche T, Krause E, Hoflack B
Proteomics (2005) 5(15): 3868-75
Snake venomics: comparative analysis of the venom proteomes of the Tunisian snakes Cerastes cerastes, Cerastes vipera and Macrovipera lebetina
Bazaa A, Marrakchi N, El Ayeb M, Sanz L, Calvete JJ
Proteomics (2005) 5(16): 4223-35
A comparative study of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis extracellular proteomes
Gohar M, Gilois N, Graveline R, Garreau C, Sanchis V, Lereclus D
Proteomics (2005) 5(14): 3696-711
Proteomics-based consensus prediction of protein retention in a bacterial membrane
Tjalsma H, van Dijl JM
Proteomics (2005) 5(17): 4472-82
Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica
Gade D, Gobom J, Rabus R
Proteomics (2005) 5(14): 3672-83
Proteomic analysis of proteins expressed by Helicobacter pylori under oxidative stress
Chuang MH, Wu MS, Lin JT, Chiou SH
Proteomics (2005) 5(15): 3895-901
Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry
Suh MJ, Hamburg DM, Gregory ST, Dahlberg AE, Limbach PA
Proteomics (2005) 5(18): 4818-31
2-D reference map of Bacillus anthracis vaccine strain A16R proteins
Wang J, Ying T, Wang H, Shi Z, Li M, He K, Feng E, Wang J, Yuan J, Li T, Wei K, Su G, Zhu H, Zhang X, Huang P, Huang L
Proteomics (2005) 5(17): 4488-95
Proteome analysis reveals adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung environment
Sriramulu DD, Nimtz M, Romling U
Proteomics (2005) 5(14): 3712-21
Global protein expression pattern of Bradyrhizobium japonicum bacteroids: a prelude to functional proteomics
Sarma AD, Emerich DW
Proteomics (2005) 5(16): 4170-84
Proteomic studies of the thylakoid membrane of Synechocystis sp. PCC 6803
Srivastava R, Pisareva T, Norling B
Proteomics (2005) 5(18): 4905-16
Immunoproteomics of outer membrane proteins and extracellular proteins of Shigella flexneri 2a 2457T
Ying T, Wang H, Li M, Wang J, Wang J, Shi Z, Feng E, Liu X, Su G, Wei K, Zhang X, Huang P, Huang L
Proteomics (2005) 5(18): 4777-93
Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins
Gade D, Theiss D, Lange D, Mirgorodskaya E, Lombardot T, Glockner FO, Kube M, Reinhardt R, Amann R, Lehrach H, Rabus R, Gobom J
Proteomics (2005) 5(14): 3654-71
Proteomics viewed on stress response of thermophilic bacterium Bacillus stearothermophilus TLS33
Topanurak S, Sinchaikul S, Phutrakul S, Sookkheo B, Chen ST
Proteomics (2005) 5(14): 3722-30
The extracellular and cytoplasmic proteomes of the non-virulent Bacillus anthracis strain UM23C1-2
Antelmann H, Williams RC, Miethke M, Wipat A, Albrecht D, Harwood CR, Hecker M
Proteomics (2005) 5(14): 3684-95
Proteomic characterization of the acid tolerance response in Lactococcus lactis MG1363
Budin-Verneuil A, Pichereau V, Auffray Y, Ehrlich DS, Maguin E
Proteomics (2005) 5(18): 4794-807
Functional proteomics and correlated signaling pathway of the thermophilic bacterium Bacillus stearothermophilus TLS33 under cold-shock stress
Topanurak S, Sinchaikul S, Sookkheo B, Phutrakul S, Chen ST
Proteomics (2005) 5(17): 4456-71
Functional subgenomics of Clostridium thermocellum cellulosomal genes: identification of the major catalytic components in the extracellular complex and detection of three new enzymes
Zverlov VV, Kellermann J, Schwarz WH
Proteomics (2005) 5(14): 3646-53
A top-down proteomics approach for differentiating thermal resistant strains of Enterobacter sakazakii
Williams TL, Monday SR, Edelson-Mammel S, Buchanan R, Musser SM
Proteomics (2005) 5(16): 4161-9
Proteome modifications of blue mussel (Mytilus edulis L.) gills as an effect of water pollution
Manduzio H, Cosette P, Gricourt L, Jouenne T, Lenz C, Andersen OK, Leboulenger F, Rocher B
Proteomics (2005) 5(18): 4958-63
Proteomic analysis of the response of human lung cells to uranium
Malard V, Prat O, Darrouzet E, Berenguer F, Sage N, Quemeneur E
Proteomics (2005) 5(17): 4568-80
Peroxisomal proteomics, a new tool for risk assessment of peroxisome proliferating pollutants in the marine environment
Mi J, Orbea A, Syme N, Ahmed M, Cajaraville MP, Cristobal S
Proteomics (2005) 5(15): 3954-65
Target identification of the novel antiobesity agent tungstate in adipose tissue from obese rats
Barcelo-Batllori S, Corominola H, Claret M, Canals I, Guinovart J, Gomis R
Proteomics (2005) 5(18): 4927-35
Surface plasmon resonance imaging-based protein arrays for high-throughput screening of protein-protein interaction inhibitors
Jung SO, Ro HS, Kho BH, Shin YB, Kim MG, Chung BH
Proteomics (2005) 5(17): 4427-31
Printing of protein microarrays via a capillary-free fluid jetting mechanism
Barron JA, Young HD, Dlott DD, Darfler MM, Krizman DB, Ringeisen BR
Proteomics (2005) 5(16): 4138-44
Application of protein lysate microarrays to molecular marker verification and quantification
Ramaswamy A, Lin E, Chen I, Mitra R, Morrisett J, Coombes K, Ju Z, Kapoor M
Proteome Sci (2005) 3(1): 9
Grating-coupled surface plasmon resonance: a cell and protein microarray platform
Unfricht DW, Colpitts SL, Fernandez SM, Lynes MA
Proteomics (2005) 5(17): 4432-42
A proteomic method for the analysis of changes in protein concentrations in response to systemic perturbations using metabolic incorporation of stable isotopes and mass spectrometry
Gustavsson N, Greber B, Kreitler T, Himmelbauer H, Lehrach H, Gobom J
Proteomics (2005) 5(14): 3563-70
Peptide microarrays for the characterization of antigenic regions of human chromogranin A
Chiari M, Cretich M, Corti A, Damin F, Pirri G, Longhi R
Proteomics (2005) 5(14): 3600-3
Surface plasmon resonance imaging-based protein arrays for high-throughput screening of protein-protein interaction inhibitors
Jung SO, Ro HS, Kho BH, Shin YB, Kim MG, Chung BH
Proteomics (2005) 5(17): 4427-31
Bioinformatics analysis for interactive proteomics
Chen Y, Xu D
Curr Protoc Protein Sci (2005) Chapter 25: Unit 25.1
Purification, stabilization, and concentration of very weak protein-protein complexes: Shifting the association equilibrium via complex selective adsorption on lowly activated supports
Fuentes M, Mateo C, Pessela BC, Guisan JM, Fernandez-Lafuente R
Proteomics (2005) 5(16): 4062-9
Performance of the computer algorithm COMPLX for the detection of protein complexes in the mass spectra of simulated biological mixtures
Wong JW, Downard KM
J Mass Spectrom (2005) 40(9): 1187-96
Improved sensitivity for quantification of proteins using triply charged cleavable isotope-coded affinity tag peptides
Qu J, Straubinger RM
Rapid Commun Mass Spectrom (2005) 19(19): 2857-64
Comparative proteomic analysis using samples obtained with laser microdissection and saturation dye labelling
Wilson KE, Marouga R, Prime JE, Pashby DP, Orange PR, Crosier S, Keith AB, Lathe R, Mullins J, Estibeiro P, Bergling H, Hawkins E, Morris CM
Proteomics (2005) 5(15): 3851-8
Quantitation in capillary electrophoresis-mass spectrometry
Ohnesorge J, Neususs C, Watzig H
Electrophoresis (2005) 26(21): 3973-87
A fast method for quantitative proteomics based on a combination between two-dimensional electrophoresis and 15N-metabolic labelling
Snijders AP, de Vos MG, de Koning B, Wright PC
Electrophoresis (2005) 26(16): 3191-9
Comparative proteomics analysis of human pituitary adenomas: current status and future perspectives
Zhan X, Desiderio DM
Mass Spectrom Rev (2005) 24(6): 783-813
Applying proteomics technology to platelet research
Garcia A, Watson SP, Dwek RA, Zitzmann N
Mass Spectrom Rev (2005) 24(6): 918-30
Liquid chromatography-mass spectrometry for the quantitative bioanalysis of anticancer drugs
Stokvis E, Rosing H, Beijnen JH
Mass Spectrom Rev (2005) 24(6): 887-917
Phosphoproteomics by mass spectrometry and classical protein chemistry approaches
Salih E
Mass Spectrom Rev (2005) 24(6): 828-46
Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies
Gulcicek EE, Colangelo CM, McMurray W, Stone K, Williams K, Wu T, Zhao H, Spratt H, Kurosky A, Wu B
Curr Protoc Bioinformatics (2005) Chapter 13: Unit 13.1
Mass spectrometry and the search for moonlighting proteins
Jeffery CJ
Mass Spectrom Rev (2005) 24(6): 772-82
Quantitation in capillary electrophoresis-mass spectrometry
Ohnesorge J, Neususs C, Watzig H
Electrophoresis (2005) 26(21): 3973-87
State-of-the-art in phosphoproteomics
Reinders J, Sickmann A
Proteomics (2005) 5(16): 4052-61
Bridging proteomics and systems biology: what are the roads to be traveled? attempts to uncover the systemic properties of biological systems
Souchelnytskyi S
Proteomics (2005) 5(16): 4123-37
Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery
Kolch W, Neususs C, Pelzing M, Mischak H
Mass Spectrom Rev (2005) 24(6): 959-77
Proteome imaging: a closer look at life's organization
Heeren RM
Proteomics (2005) 5(17): 4316-26
Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins
Moritz RL, Clippingdale AB, Kapp EA, Eddes JS, Ji H, Gilbert S, Connolly LM, Simpson RJ
Proteomics (2005) 5(13): 3402-13
Assessment of microwave-assisted enzymatic digestion by measuring glycated hemoglobin A1c by mass spectrometry
Vesper HW, Mi L, Enada A, Myers GL
Rapid Commun Mass Spectrom (2005) 19(19): 2865-70
Two-dimensional benzyldimethyl-n-hexadecylammonium chloride/SDS-PAGE for membrane proteomics
Zahedi RP, Meisinger C, Sickmann A
Proteomics (2005) 5(14): 3581-8
An enhanced method for peptides sequencing by N-terminal derivatization and MS
Noga MJ, Lewandowski JJ, Suder P, Silberring J
Proteomics (2005) 5(17): 4367-75
Multiplex multidimensional nanoLC-MS system for targeted proteomic analyses
Bonneil E, Tessier S, Carrier A, Thibault P
Electrophoresis (2005) 26(24): 4575-89
Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data
Haab BB, Geierstanger BH, Michailidis G, Vitzthum F, Forrester S, Okon R, Saviranta P, Brinker A, Sorette M, Perlee L, Suresh S, Drwal G, Adkins JN, Omenn GS
Proteomics (2005) 5(13): 3278-91
Dansylation of tryptic peptides for increased sequence coverage in protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric peptide mass fingerprinting
Park SJ, Song JS, Kim HJ
Rapid Commun Mass Spectrom (2005) 19(21): 3089-96
Nanostructures and molecular force bases of a highly sensitive capacitive immunosensor
Zeng G, Yang P, Zheng Z, Feng Q, Cai J, Zhang S, Chen ZW
Proteomics (2005) 5(17): 4347-53
Large-scale protein expression for proteome research
Korf U, Kohl T, van der Zandt H, Zahn R, Schleeger S, Ueberle B, Wandschneider S, Bechtel S, Schnolzer M, Ottleben H, Wiemann S, Poustka A
Proteomics (2005) 5(14): 3571-80
Immunodepletion of albumin for two-dimensional gel detection of new mouse acute-phase protein and other plasma proteins
Duan X, Yarmush D, Berthiaume F, Jayaraman A, Yarmush ML
Proteomics (2005) 5(15): 3991-4000
Effective removal of albumin from serum
Colantonio DA, Dunkinson C, Bovenkamp DE, Van Eyk JE
Proteomics (2005) 5(15): 3831-5
Two-dimensional liquid chromatography/tandem mass spectrometry analysis of Gradiflow fractionated native human plasma
Wasinger VC, Locke VL, Raftery MJ, Larance M, Rothemund D, Liew A, Bate I, Guilhaus M
Proteomics (2005) 5(13): 3397-401
A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes
Tang HY, Ali-Khan N, Echan LA, Levenkova N, Rux JJ, Speicher DW
Proteomics (2005) 5(13): 3329-42
Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery
Kolch W, Neususs C, Pelzing M, Mischak H
Mass Spectrom Rev (2005) 24(6): 959-77
Albumin depletion of human plasma also removes low abundance proteins including the cytokines
Granger J, Siddiqui J, Copeland S, Remick D
Proteomics (2005) 5(18): 4713-8
Proteomic analysis of mouse liver plasma membrane: use of differential extraction to enrich hydrophobic membrane proteins
Zhang L, Xie J, Wang X, Liu X, Tang X, Cao R, Hu W, Nie S, Fan C, Liang S
Proteomics (2005) 5(17): 4510-24
Advantages and limitations of clear-native PAGE
Wittig I, Schagger H
Proteomics (2005) 5(17): 4338-46
Protein profiling by microscale solution isoelectrofocusing (MicroSol-IEF)
Zuo X, Lee K, Ali-Khan N, Speicher DW
Curr Protoc Protein Sci (2005) Chapter 22: Unit 22.6
A proteomics strategy for the enrichment of receptor-associated complexes
Cross M, Nguyen T, Bogdanoska V, Reynolds E, Hamilton JA
Proteomics (2005) 5(18): 4754-63
Grating-coupled surface plasmon resonance: a cell and protein microarray platform
Unfricht DW, Colpitts SL, Fernandez SM, Lynes MA
Proteomics (2005) 5(17): 4432-42
Rapid enrichment of bioactive milk proteins and iterative, consolidated protein identification by multidimensional protein identification technology
Panchaud A, Kussmann M, Affolter M
Proteomics (2005) 5(15): 3836-46
Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform
Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, Hung MC, Kuerer HM
Proteomics (2005) 5(16): 4107-17
Performance validation of an improved Xenon-arc lamp-based CCD camera system for multispectral imaging in proteomics
Scrivener E, Boghigian BA, Golenko E, Bogdanova A, Jackson P, Mikulskis A, Denoyer E, Courtney P, Lopez MF, Patton WF
Proteomics (2005) 5(17): 4354-66
Direct chemiluminescent imaging detection of Cu/Zn-superoxidase dismutase, glutathione peroxidase, carbonic anhydrase-III, and catalase in rat liver cytosol separated by native porous gradient polyacrylamide gel electrophoresis
Chen H, Zhao H, Huang L, Baeyens WR, Delanghe JR, He D, Ouyang J
Electrophoresis (2005) 26(22): 4260-9
Evaluation of several two-dimensional gel electrophoresis techniques in cardiac proteomics
Li ZB, Flint PW, Boluyt MO
Electrophoresis (2005) 26(18): 3572-85
Printing of protein microarrays via a capillary-free fluid jetting mechanism
Barron JA, Young HD, Dlott DD, Darfler MM, Krizman DB, Ringeisen BR
Proteomics (2005) 5(16): 4138-44
Nonaqueous capillary electrophoresis in coated capillaries: an interesting alternative for proteomic applications
Assuncao NA, Deziderio LA, Paulino LG, Lupetti KO, Carrilho E
Electrophoresis (2005) 26(17): 3292-9
Improved sensitivity for quantification of proteins using triply charged cleavable isotope-coded affinity tag peptides
Qu J, Straubinger RM
Rapid Commun Mass Spectrom (2005) 19(19): 2857-64
On the accuracy of polypeptide masses measured in a linear ion trap
Gorshkov MV, Zubarev RA
Rapid Commun Mass Spectrom (2005) 19(24): 3755-8
Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma
Echan LA, Tang HY, Ali-Khan N, Lee K, Speicher DW
Proteomics (2005) 5(13): 3292-303
Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis
Huang L, Harvie G, Feitelson JS, Gramatikoff K, Herold DA, Allen DL, Amunngama R, Hagler RA, Pisano MR, Zhang WW, Fang X
Proteomics (2005) 5(13): 3314-28
Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC
Gevaert K, Staes A, Van Damme J, De Groot S, Hugelier K, Demol H, Martens L, Goethals M, Vandekerckhove J
Proteomics (2005) 5(14): 3589-99
Variable low-mass filtering using an electrodynamic ion funnel
Page JS, Tolmachev AV, Tang K, Smith RD
J Mass Spectrom (2005) 40(9): 1215-22
Proteome imaging: a closer look at life's organization
Heeren RM
Proteomics (2005) 5(17): 4316-26
Differences among techniques for high-abundant protein depletion
Zolotarjova N, Martosella J, Nicol G, Bailey J, Boyes BE, Barrett WC
Proteomics (2005) 5(13): 3304-13
On-target trypsinization on MALDI target for MS
Kajiwara H
J Mass Spectrom (2005) 40(11): 1503-4
Enhanced phosphopeptide isolation by Fe(III)-IMAC using 1,1,1,3,3,3-hexafluoroisopropanol
Barnouin KN, Hart SR, Thompson AJ, Okuyama M, Waterfield M, Cramer R
Proteomics (2005) 5(17): 4376-88
A proteomic method for the analysis of changes in protein concentrations in response to systemic perturbations using metabolic incorporation of stable isotopes and mass spectrometry
Gustavsson N, Greber B, Kreitler T, Himmelbauer H, Lehrach H, Gobom J
Proteomics (2005) 5(14): 3563-70
Analysis of proteins from a glioma cell line by using micro-scale solution isoelectric focusing in combination with liquid chromatography/tandem mass spectrometry
Westman-Brinkmalm A, Karlsson G, Brive LM, Hedberg-Fogel K, Persson R, Karlsson H, Ekman R, Blennow K
Rapid Commun Mass Spectrom (2005) 19(24): 3651-8
Isolation of viral ribonucleoprotein complexes from infected cells by tandem affinity purification
Mayer D, Baginsky S, Schwemmle M
Proteomics (2005) 5(17): 4483-7
Human serum and plasma proteomics
Musselman I, Speicher DW
Curr Protoc Protein Sci (2005) Chapter 24: Unit 24.1
Isoelectric focusing in serial immobilized pH gradient gels to improve protein separation in proteomic analysis
Poznanovic S, Schwall G, Zengerling H, Cahill MA
Electrophoresis (2005) 26(16): 3185-90
Self-made frits for nanoscale columns in proteomics
Maiolica A, Borsotti D, Rappsilber J
Proteomics (2005) 5(15): 3847-50
Utility of electrophoretically derived protein mass estimates as additional constraints in proteome analysis of human serum based on MS/MS analysis
Kim JY, Lee JH, Park GW, Cho K, Kwon KH, Park YM, Cho SY, Paik YK, Yoo JS
Proteomics (2005) 5(13): 3376-85
Human urine proteome analysis by three separation approaches
Sun W, Li F, Wu S, Wang X, Zheng D, Wang J, Gao Y
Proteomics (2005) 5(18): 4994-5001
Evaluation of prefractionation methods as a preparatory step for multidimensional based chromatography of serum proteins
Barnea E, Sorkin R, Ziv T, Beer I, Admon A
Proteomics (2005) 5(13): 3367-75
Fluoroprofile, a fluorescence-based assay for rapid and sensitive quantitation of proteins in solution
Mackintosh JA, Veal DA, Karuso P
Proteomics (2005) 5(18): 4673-7
Development of a simplified, economical polyacrylamide gel staining protocol for phosphoproteins
Agrawal GK, Thelen JJ
Proteomics (2005) 5(18): 4684-8
Application of protein lysate microarrays to molecular marker verification and quantification
Ramaswamy A, Lin E, Chen I, Mitra R, Morrisett J, Coombes K, Ju Z, Kapoor M
Proteome Sci (2005) 3: 9
A strategy for distinguishing modified peptides based on post-digestion 18O labeling and mass spectrometry
Sun G, Anderson VE
Rapid Commun Mass Spectrom (2005) 19(19): 2849-56
Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map
Cho SY, Lee EY, Lee JS, Kim HY, Park JM, Kwon MS, Park YK, Lee HJ, Kang MJ, Kim JY, Yoo JS, Park SJ, Cho JW, Kim HS, Paik YK
Proteomics (2005) 5(13): 3386-96
Two-dimensional gel isoelectric focusing
Stastna M, Slais K
Electrophoresis (2005) 26(18): 3586-91
Simple and effective technical procedures for the packing and application of nanospray PicoFrit HPLC columns for proteomic analyses
Howells LC, Whelan AO, Woodward MJ, Coldham NG
Proteomics (2005) 5(15): 3864-7
A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system
Misek DE, Kuick R, Wang H, Galchev V, Deng B, Zhao R, Tra J, Pisano MR, Amunugama R, Allen D, Walker AK, Strahler JR, Andrews P, Omenn GS, Hanash SM
Proteomics (2005) 5(13): 3343-52
Rapid on-membrane proteolytic cleavage for Edman sequencing and mass spectrometric identification of proteins
Pham VC, Henzel WJ, Lill JR
Electrophoresis (2005) 26(22): 4243-51
Purification, stabilization, and concentration of very weak protein-protein complexes: Shifting the association equilibrium via complex selective adsorption on lowly activated supports
Fuentes M, Mateo C, Pessela BC, Guisan JM, Fernandez-Lafuente R
Proteomics (2005) 5(16): 4062-9
Biological tissue imaging with time-of-flight secondary ion mass spectrometry and cluster ion sources
Brunelle A, Touboul D, Laprevote O
J Mass Spectrom (2005) 40(8): 985-99
HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples
Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, Mehigh RJ, Cockrill SL, Scott GB, Tammen H, Schulz-Knappe P, Speicher DW, Vitzthum F, Haab BB, Siest G, Chan DW
Proteomics (2005) 5(13): 3262-77
Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project
Li X, Gong Y, Wang Y, Wu S, Cai Y, He P, Lu Z, Ying W, Zhang Y, Jiao L, He H, Zhang Z, He F, Zhao X, Qian X
Proteomics (2005) 5(13): 3423-41
A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy
Adkins JN, Monroe ME, Auberry KJ, Shen Y, Jacobs JM, Camp DG 2nd, Vitzthum F, Rodland KD, Zangar RC, Smith RD, Pounds JG
Proteomics (2005) 5(13): 3454-66
Dye-free protein molecular weight markers
Chang M, Hsu HY, Lee HJ
Electrophoresis (2005) 26(16): 3062-8
Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines
Shadforth I, Crowther D, Bessant C
Proteomics (2005) 5(16): 4082-95
Enrichment of phosphorylated proteins and peptides from complex mixtures using metal oxide/hydroxide affinity chromatography (MOAC)
Wolschin F, Wienkoop S, Weckwerth W
Proteomics (2005) 5(17): 4389-97
From proteins to systems: the British Society for Proteomics Research (BSPR) meeting 2005
McIntyre SF
Proteomics (2005) 5(15): 3828-30
Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005)
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK Jr, Apweiler R
Proteomics (2005) 5(14): 3552-5
HUPO BPP Workshop on Mouse Models for Neurodegeneration--Choosing the right models
Hamacher M, Marcus K, Stephan C, van Hall A, Meyer HE
Proteomics (2005) 5(14): 3558-9
Report on the 1st International Conference of the Hellenic Proteomics Society in Athens, Greece
Fountoulakis M, Vlahou A
Proteomics (2005) 5(14): 3556-7
5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame
Stephan C, Hamacher M, Bluggel M, Korting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schafer H, Martens L, Jones P, Muller M, Auyeung K, Taylor C, Binz PA, Thiele H, Parkinson D, Meyer HE, Apweiler R
Proteomics (2005) 5(14): 3560-2
The European Proteomics Association (EuPA) is in the field. Report of the formal inauguration of the European Proteome Association (Munich, Germany, August 29, 2005)
Kleinhammer C, Corthals GL
Proteomics (2005) 5(18): 4648-50
Rules governing protein identification by mass spectrometry
Taylor GK, Goodlett DR
Rapid Commun Mass Spectrom (2005) 19(23): 3420
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K
Proteomics (2005) 5(13): 3501-5