Volume 7; Issue 1

Journal of Proteome Research

Volume 7; Issue 1

1

Large-Scale Identification and Evolution Indexing of Tyrosine Phosphorylation Sites from Murine Brain

Ballif, Bryan A., Carey, G. Richard, Sunyaev, Shamil R., Gygi, Steven P.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2008

2

Integrated Analysis of the Cerebrospinal Fluid Peptidome and Proteome

Zougman, Alexandre, Pilch, Bartosz, Podtelejnikov, Alexandre, Kiehntopf, Michael, Schnabel, Claudia, Kumar, Chanchal, Mann, Matthias

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 3.25 MB

english, 2008

3

Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling

Choi, Hyungwon, Ghosh, Debashis, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 240 KB

english, 2008

4

Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics

Choi, Hyungwon, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 790 KB

english, 2008

5

Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing

Klie, Sebastian, Martens, Lennart, Vizcaíno, Juan Antonio, Côté, Richard, Jones, Phil, Apweiler, Rolf, Hinneburg, Alexander, Hermjakob, Henning

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 871 KB

english, 2008

6

Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results

Yu, Weichaun, He, Zengyou, Liu, Junfeng, Zhao, Hongyu

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.61 MB

english, 2008

7

Identification of Mouse Embryonic Stem Cell-Associated Proteins

Baharvand, Hossein, Fathi, Ali, Gourabi, Hamid, Mollamohammadi, Sepideh, Salekdeh, Ghasem Hosseini

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.43 MB

english, 2008

8

Proteomic Analysis of Human Follicular Fluid Using an Alternative Bottom-Up Approach

Hanrieder, Jörg, Nyakas, Adrien, Naessén, Tord, Bergquist, Jonas

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 231 KB

english, 2008

9

A Proteome Resource of Ovarian Cancer Ascites: Integrated Proteomic and Bioinformatic Analyses To Identify Putative Biomarkers

Gortzak-Uzan, Limor, Ignatchenko, Alex, Evangelou, Andreas I., Agochiya, Mahima, Brown, Kevin A., St.Onge, Peter, Kireeva, Inga, Schmitt-Ulms, Gerold, Brown, Theodore J., Murphy, Joan, Rosen, Barry, S

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.61 MB

english, 2008

10

An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data

Mueller, Lukas N., Brusniak, Mi-Youn, Mani, D. R., Aebersold, Ruedi

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 592 KB

english, 2008

11

Statistical Analysis of Relative Labeled Mass Spectrometry Data from Complex Samples Using ANOVA

Oberg, Ann L., Mahoney, Douglas W., Eckel-Passow, Jeanette E., Malone, Christopher J., Wolfinger, Russell D., Hill, Elizabeth G., Cooper, Leslie T., Onuma, Oyere K., Spiro, Craig, Therneau, Terry M.,

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 632 KB

english, 2008

12

Analysis of Host-Inducing Proteome Changes in Bifidobacterium longum NCC2705 Grown in Vivo

Yuan, Jing, Wang, Bin, Sun, Zhongke, Bo, Xin, Yuan, Xitong, He, Xiang, Zhao, Hongqing, Du, Xinying, Wang, Fang, Jiang, Zheng, Zhang, Ling, Jia, Leili, Wang, Yufei, Wei, KaiHua, Wang, Jie, Zhang, Xuemi

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2008

13

In Silico Tools for Predicting Peptides Binding to HLA-Class II Molecules: More Confusion than Conclusion

Gowthaman, Uthaman, Agrewala, Javed N.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 757 KB

english, 2008

14

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

Käll, Lukas, Storey, John D., MacCoss, Michael J., Noble, William Stafford

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2008

15

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

Käll, Lukas, Storey, John D., MacCoss, Michael J., Noble, William Stafford

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 275 KB

english, 2008

16

Does Trypsin Cut Before Proline?

Rodriguez, Jesse, Gupta, Nitin, Smith, Richard D., Pevzner, Pavel A.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 889 KB

english, 2008

17

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

Searle, Brian C., Turner, Mark, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.47 MB

english, 2008

18

Occurrence of Copper Proteins through the Three Domains of Life: A Bioinformatic Approach

Andreini, Claudia, Banci, Lucia, Bertini, Ivano, Rosato, Antonio

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 632 KB

english, 2008

19

False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics

Choi, Hyungwon, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 82 KB

english, 2008

20

Interactive Three-Dimensional Visualization and Contextual Analysis of Protein Interaction Networks

Ho, Edwin, Webber, Richard, Wilkins, Marc R.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2008

21

Clustering Millions of Tandem Mass Spectra

Frank, Ari M., Bandeira, Nuno, Shen, Zhouxin, Tanner, Stephen, Briggs, Steven P., Smith, Richard D., Pevzner, Pavel A.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 813 KB

english, 2008

22

On the Value of Knowing a z• Ion for What It Is

Liu, Jian, Liang, Xiaorong, McLuckey, Scott A.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 293 KB

english, 2008

23

Metabolomic and Proteomic Analysis of a Clonal Insulin-Producing β-Cell Line (INS-1 832/13)

Fernandez, Céline, Fransson, Ulrika, Hallgard, Elna, Spégel, Peter, Holm, Cecilia, Krogh, Morten, Wårell, Kristofer, James, Peter, Mulder, Hindrik

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 325 KB

english, 2008

24

Modes of Inference for Evaluating the Confidence of Peptide Identifications

Fitzgibbon, Matt, Li, Qunhua, McIntosh, Martin

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 822 KB

english, 2008

25

Accurate Annotation of Peptide Modifications through Unrestrictive Database Search

Tanner, Stephen, Payne, Samuel H., Dasari, Surendra, Shen, Zhouxin, Wilmarth, Phillip A., David, Larry L., Loomis, William F., Briggs, Steven P., Bafna, Vineet

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 792 KB

english, 2008

26

Deriving the Probabilities of Water Loss and Ammonia Loss for Amino Acids from Tandem Mass Spectra

Sun, Shiwei, Yu, Chungong, Qiao, Yantao, Lin, Yu, Dong, Gongjin, Liu, Changning, Zhang, Jingfen, Zhang, Zhuo, Cai, Jinjin, Zhang, Hong, Bu, Dongbo

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 905 KB

english, 2008

27

A powerful tool for PTM discovery

Cassiday, Laura

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 98 KB

english, 2008

28

Antiviral Phagocytosis Is Regulated by a Novel Rab-Dependent Complex in Shrimp Penaeus japonicus

Wu, Wenlin, Zong, Rongrong, Xu, Jianyang, Zhang, Xiaobo

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2008

29

Proteomics Projects: HAI brings antibody researchers together

Cottingham, Katie

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 217 KB

english, 2008

30

Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose Repression Saccharomyces cerevisiae Strains: The Comparison of Two Quantitative Methods

Usaite, Renata, Wohlschlegel, James, Venable, John D., Park, Sung K., Nielsen, Jens, Olsson, Lisbeth, Yates III, John R.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 380 KB

english, 2008

31

Data Augmentation Algorithms for Detecting Conserved Domains in Protein Sequences: A Comparative Study

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 3.06 MB

english, 2008

32

Aqueous Polymer Two-Phase Systems for the Proteomic Analysis of Plasma Membranes from Minute Brain Samples

Schindler, Jens, Lewandrowski, Urs, Sickmann, Albert, Friauf, Eckhard

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 438 KB

english, 2008

33

Quantitation by Isobaric Labeling: Applications to Glycomics

Atwood, James A., Cheng, Lei, Alvarez-Manilla, Gerardo, Warren, Nicole L., York, William S., Orlando, Ron

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 2.36 MB

english, 2008

34

Proteome of Murine Jejunal Brush Border Membrane Vesicles

Donowitz, Mark, Singh, Siddharth, Salahuddin, Farah F., Hogema, Boris M., Chen, Yueping, Gucek, Marjan, Cole, Robert N., Ham, Amy, Zachos, Nicholas C., Kovbasnjuk, Olga, Lapierre, Lynne A., Broere, Ne

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 32 KB

english, 2008

35

Biomarker Discovery for Arsenic Exposure Using Functional Data. Analysis and Feature Learning of Mass Spectrometry Proteomic Data

Harezlak, Jaroslaw, Wu, Michael C., Wang, Mike, Schwartzman, Armin, Christiani, David C., Lin, Xihong

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 547 KB

english, 2008

36

Online Multidimensional Separation with Biphasic Monolithic Capillary Column for Shotgun Proteome Analysis

Wang, Fangjun, Dong, Jing, Ye, Mingliang, Jiang, Xiaogang, Wu, Ren’an, Zou, Hanfa

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 879 KB

english, 2008

37

The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools

Klimek, John, Eddes, James S., Hohmann, Laura, Jackson, Jennifer, Peterson, Amelia, Letarte, Simon, Gafken, Philip R., Katz, Jonathan E, Mallick, Parag, Lee, Hookeun, Schmidt, Alexander, Ossola, Reto,

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 558 KB

english, 2008

38

People: New Editorial Advisory Board members

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 142 KB

english, 2008

39

A Data-Mining Scheme for Identifying Peptide Structural Motifs Responsible for Different MS/MS Fragmentation Intensity Patterns

Huang, Yingying, Tseng, George C., Yuan, Shinsheng, Pasa-Tolic, Ljiljana, Lipton, Mary S., Smith, Richard D., Wysocki, Vicki H.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 2.39 MB

english, 2008

40

Identification and Characterization of Disulfide Bonds in Proteins and Peptides from Tandem MS Data by Use of the MassMatrix MS/MS Search Engine

Xu, Hua, Zhang, Liwen, Freitas, Michael A.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 210 KB

english, 2008

41

Algorithm for Identification of Fusion Proteins via Mass Spectrometry

Ng, Julio, Pevzner, Pavel A.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2008

42

Design of Recombinant Antibody Microarrays for Cell Surface Membrane Proteomics

Dexlin, Linda, Ingvarsson, Johan, Frendéus, Björn, Borrebaeck, Carl A. K., Wingren, Christer

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2008

43

Simultaneous Analysis of Circulating Human Cytokines Using a High-Sensitivity Cytokine Biochip Array

FitzGerald, S. Pete, McConnell, R. Ivan, Huxley, Allen

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2008

44

What’s Driving False Discovery Rates?

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 58 KB

english, 2008

45

Meetings

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 72 KB

english, 2008

46

High-Accuracy Peptide Mass Fingerprinting Using Peak Intensity Data with Machine Learning

Yang, Dongmei, Ramkissoon, Kevin, Hamlett, Eric, Giddings, Morgan C.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2008

47

Protein Identification and Peptide Expression Resolver: Harmonizing Protein Identification with Protein Expression Data

Kearney, Paul, Butler, Heather, Eng, Kevin, Hugo, Patrice

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2008

48

Developing and Disseminating Advances in Computational and Statistical Proteomics

McIntosh, Martin

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 82 KB

english, 2008

49

Local and Nonlocal Environments around Cis Peptides

Wathen, Brent, Jia, Zongchao

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 126 KB

english, 2008

50

X!!Tandem, an Improved Method for Running X!Tandem in Parallel on Collections of Commodity Computers

Bjornson, Robert D., Carriero, Nicholas J., Colangelo, Christopher, Shifman, Mark, Cheung, Kei-Hoi, Miller, Perry L., Williams, Kenneth

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 689 KB

english, 2008

51

The Effects of Shared Peptides on Protein Quantitation in Label-Free Proteomics by LC/MS/MS

Jin, Shuangshuang, Daly, Donald S., Springer, David L., Miller, John H.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 434 KB

english, 2008

52

Species Variation in the Fecal Metabolome Gives Insight into Differential Gastrointestinal Function

Saric, Jasmina, Wang, Yulan, Li, Jia, Coen, Muireann, Utzinger, Jürg, Marchesi, Julian R., Keiser, Jennifer, Veselkov, Kirill, Lindon, John C., Nicholson, Jeremy K., Holmes, Elaine

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.12 MB

english, 2008

53

Ovarian cancer proteins identified with microarrays | Potential biomarker for neural progenitor cells | Enhanced ion charge states for ETD | Calorimetry for proteomics | Quantitative analysis of protein complexes | Tea tasters replaced by NMR? | Percolator | The biochemical network database | Mass spectrum quality assessment | Getting the most out of MS 2 and MS 3 data

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 230 KB

english, 2008

54

Real-Time Fluorescence Monitoring of Tryptic Digestion in Proteomics

Karuso, Peter, Crawford, Angela S., Veal, Duncan A., Scott, Graham B. I., Choi, Hung-Yoon

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 669 KB

english, 2008

55

Turning data graveyards into gold mines

Cottingham, Katie

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 142 KB

english, 2008

56

Signal Detection in High-Resolution Mass Spectrometry Data

McLerran, Dale F., Feng, Ziding, Semmes, O. John, Cazares, Lisa, Randolph, Timothy W.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2008

57

New Products

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 116 KB

english, 2008

58

Whole Genome Searching with Shotgun Proteomic Data: Applications for Genome Annotation

Sevinsky, Joel R., Cargile, Benjamin J., Bunger, Maureen K., Meng, Fanyu, Yates, Nathan A., Hendrickson, Ronald C., Stephenson, Jr., James L.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.68 MB

english, 2008

59

A Quantitative Proteomic Analysis of Mitochondrial Participation in P19 Cell Neuronal Differentiation

Watkins, Jermel, Basu, Siddhartha, Bogenhagen, Daniel F.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2008