-
1
-
-
84941051862
-
The human dental pulp proteome and N-Terminome: levering the unexplored potential of semitryptic peptides enriched by TAILS to identify missing proteins in the human proteome project in underexplored tissues
-
Eckhard U., Marino G., Abbey S.R., Tharmarajah G., Matthew I., Overall C.M. The human dental pulp proteome and N-Terminome: levering the unexplored potential of semitryptic peptides enriched by TAILS to identify missing proteins in the human proteome project in underexplored tissues. J. Proteome Res. 2015, 14:3568-3582. 10.1021/acs.jproteome.5b00579.
-
(2015)
J. Proteome Res.
, vol.14
, pp. 3568-3582
-
-
Eckhard, U.1
Marino, G.2
Abbey, S.R.3
Tharmarajah, G.4
Matthew, I.5
Overall, C.M.6
-
2
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567. 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2.
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
-
3
-
-
3142702204
-
TANDEM: matching proteins with tandem mass spectra
-
Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467. 10.1093/bioinformatics/bth092.
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
4
-
-
84872371907
-
Comet: an open-source MS/MS sequence database search tool
-
Eng J.K., Jahan T.A., Hoopmann M.R. Comet: an open-source MS/MS sequence database search tool. Proteomics 2013, 13:22-24. 10.1002/pmic.201200439.
-
(2013)
Proteomics
, vol.13
, pp. 22-24
-
-
Eng, J.K.1
Jahan, T.A.2
Hoopmann, M.R.3
-
5
-
-
84923247212
-
MS-GF+ makes progress towards a universal database search tool for proteomics
-
Kim S., Pevzner P.A. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat. Commun. 2014, 5:5277. 10.1038/ncomms6277.
-
(2014)
Nat. Commun.
, vol.5
, pp. 5277
-
-
Kim, S.1
Pevzner, P.A.2
-
6
-
-
80053404377
-
Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates
-
Kleifeld O., Doucet A., Prudova A., auf dem Keller U., Gioia M., Kizhakkedathu J.N., et al. Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates. Nat. Protoc. 2011, 6:1578-1611. 10.1038/nprot.2011.382.
-
(2011)
Nat. Protoc.
, vol.6
, pp. 1578-1611
-
-
Kleifeld, O.1
Doucet, A.2
Prudova, A.3
Auf dem Keller, U.4
Gioia, M.5
Kizhakkedathu, J.N.6
-
7
-
-
77749320923
-
Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products
-
Kleifeld O., Doucet A., auf dem Keller U., Prudova A., Schilling O., Kainthan R.K., et al. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat. Biotechnol. 2010, 28:281-288. 10.1038/nbt.1611.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 281-288
-
-
Kleifeld, O.1
Doucet, A.2
Auf dem Keller, U.3
Prudova, A.4
Schilling, O.5
Kainthan, R.K.6
-
8
-
-
84919472207
-
TAILS N-terminomics of human platelets reveals pervasive metalloproteinase dependent proteolytic processing in storage
-
blood-2014-04-569640
-
Prudova A., Serrano K., Eckhard U., Fortelny N., Devine D.V., Overall C.M. TAILS N-terminomics of human platelets reveals pervasive metalloproteinase dependent proteolytic processing in storage. Blood 2014, blood-2014-04-569640. 10.1182/blood-2014-04-569640.
-
(2014)
Blood
-
-
Prudova, A.1
Serrano, K.2
Eckhard, U.3
Fortelny, N.4
Devine, D.V.5
Overall, C.M.6
-
9
-
-
84872593231
-
Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation
-
rs2-rs2
-
Auf dem Keller U., Prudova A., Eckhard U., Fingleton B., Overall C.M. Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation. Sci. Signal. 2013, 6. rs2-rs2. 10.1126/scisignal.2003512.
-
(2013)
Sci. Signal.
, vol.6
-
-
Auf dem Keller, U.1
Prudova, A.2
Eckhard, U.3
Fingleton, B.4
Overall, C.M.5
-
10
-
-
77951134556
-
Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics
-
Prudova A., auf dem Keller U., Butler G.S., Overall C.M. Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics. Mol. Cell. Proteomics 2010, 9:894-911. 10.1074/mcp.M000050-MCP201.
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 894-911
-
-
Prudova, A.1
Auf dem Keller, U.2
Butler, G.S.3
Overall, C.M.4
-
11
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74:5383-5392.
-
(2002)
Anal. Chem.
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
12
-
-
80053387432
-
IProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
-
M111.007690
-
Shteynberg D., Deutsch E.W., Lam H., Eng J.K., Sun Z., Tasman N., et al. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol. Cell. Proteomics 2011, 10. M111.007690. 10.1074/mcp.M111.007690.
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Shteynberg, D.1
Deutsch, E.W.2
Lam, H.3
Eng, J.K.4
Sun, Z.5
Tasman, N.6
-
13
-
-
0042338362
-
A statistical model for identifying proteins by tandem mass spectrometry
-
Nesvizhskii A.I., Keller A., Kolker E., Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75:4646-4658.
-
(2003)
Anal. Chem.
, vol.75
, pp. 4646-4658
-
-
Nesvizhskii, A.I.1
Keller, A.2
Kolker, E.3
Aebersold, R.4
-
14
-
-
84948987628
-
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics
-
Deutsch E.W., Mendoza L., Shteynberg D., Slagel J., Sun Z., Moritz R.L. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin. Appl. 2015, 10.1002/prca.201400164.
-
(2015)
Proteomics Clin. Appl.
-
-
Deutsch, E.W.1
Mendoza, L.2
Shteynberg, D.3
Slagel, J.4
Sun, Z.5
Moritz, R.L.6
-
15
-
-
33847401893
-
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
-
Tabb D.L., Fernando C.G., Chambers M.C. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 2007, 6:654-661. 10.1021/pr0604054.
-
(2007)
J. Proteome Res.
, vol.6
, pp. 654-661
-
-
Tabb, D.L.1
Fernando, C.G.2
Chambers, M.C.3
-
16
-
-
84905397897
-
MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra
-
Dorfer V., Pichler P., Stranzl T., Stadlmann J., Taus T., Winkler S., et al. MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra. J. Proteome Res. 2014, 13:3679-3684. 10.1021/pr500202e.
-
(2014)
J. Proteome Res.
, vol.13
, pp. 3679-3684
-
-
Dorfer, V.1
Pichler, P.2
Stranzl, T.3
Stadlmann, J.4
Taus, T.5
Winkler, S.6
-
17
-
-
7044246160
-
Open mass spectrometry search algorithm
-
Geer L.Y., Markey S.P., Kowalak J.A., Wagner L., Xu M., Maynard D.M., et al. Open mass spectrometry search algorithm. J. Proteome Res. 2004, 3:958-964. 10.1021/pr0499491.
-
(2004)
J. Proteome Res.
, vol.3
, pp. 958-964
-
-
Geer, L.Y.1
Markey, S.P.2
Kowalak, J.A.3
Wagner, L.4
Xu, M.5
Maynard, D.M.6
-
18
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26:1367-1372. 10.1038/nbt.1511.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
19
-
-
84923897273
-
PeptideShaker enables reanalysis of MS-derived proteomics data sets
-
Vaudel M., Burkhart J.M., Zahedi R.P., Oveland E., Berven F.S., Sickmann A., et al. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat. Biotechnol. 2015, 33:22-24. 10.1038/nbt.3109.
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 22-24
-
-
Vaudel, M.1
Burkhart, J.M.2
Zahedi, R.P.3
Oveland, E.4
Berven, F.S.5
Sickmann, A.6
-
20
-
-
77949695293
-
Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies
-
Searle B.C. Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics 2010, 10:1265-1269. 10.1002/pmic.200900437.
-
(2010)
Proteomics
, vol.10
, pp. 1265-1269
-
-
Searle, B.C.1
-
21
-
-
84939826366
-
Protein Termini and Their Modifications Revealed by Positional Proteomics
-
Marino G., Eckhard U., Overall C.M. Protein Termini and Their Modifications Revealed by Positional Proteomics. ACS Chem. Biol. 2015, 10:1754-1764. 10.1021/acschembio.5b00189.
-
(2015)
ACS Chem. Biol.
, vol.10
, pp. 1754-1764
-
-
Marino, G.1
Eckhard, U.2
Overall, C.M.3
-
22
-
-
84909619767
-
Protein amino-terminal modifications and proteomic approaches for N-terminal profiling
-
Lai Z.W., Petrera A., Schilling O. Protein amino-terminal modifications and proteomic approaches for N-terminal profiling. Curr. Opin. Chem. Biol. 2015, 24:71-79. 10.1016/j.cbpa.2014.10.026.
-
(2015)
Curr. Opin. Chem. Biol.
, vol.24
, pp. 71-79
-
-
Lai, Z.W.1
Petrera, A.2
Schilling, O.3
-
23
-
-
84896969045
-
Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome
-
Lange P.F., Huesgen P.F., Nguyen K., Overall C.M. Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J. Proteome Res. 2014, 13:2028-2044. 10.1021/pr401191w.
-
(2014)
J. Proteome Res.
, vol.13
, pp. 2028-2044
-
-
Lange, P.F.1
Huesgen, P.F.2
Nguyen, K.3
Overall, C.M.4
-
24
-
-
84946069451
-
UniProt: a hub for protein information
-
UniProt Consortium UniProt: a hub for protein information. Nucleic Acids Res. 2015, 43:D204-D212. 10.1093/nar/gku989.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D204-D212
-
-
-
25
-
-
84941086837
-
Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events
-
Fortelny N., Yang S., Pavlidis P., Lange P.F., Overall C.M. Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. Nucleic Acids Res. 2015, 43:D290-D297. 10.1093/nar/gku1012.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D290-D297
-
-
Fortelny, N.1
Yang, S.2
Pavlidis, P.3
Lange, P.F.4
Overall, C.M.5
-
26
-
-
80052290625
-
TopFIND, a knowledgebase linking protein termini with function
-
Lange P.F., Overall C.M. TopFIND, a knowledgebase linking protein termini with function. Nat. Methods 2011, 8:703-704. 10.1038/nmeth.1669.
-
(2011)
Nat. Methods
, vol.8
, pp. 703-704
-
-
Lange, P.F.1
Overall, C.M.2
-
27
-
-
84862227658
-
TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function
-
Lange P.F., Huesgen P.F., Overall C.M. TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res. 2012, 40:D351-D361. 10.1093/nar/gkr1025.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D351-D361
-
-
Lange, P.F.1
Huesgen, P.F.2
Overall, C.M.3
-
28
-
-
80053621170
-
Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites
-
Schilling O., auf dem Keller U., Overall C.M. Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites. Biol. Chem. 2011, 392:1031-1037. 10.1515/BC.2011.158.
-
(2011)
Biol. Chem.
, vol.392
, pp. 1031-1037
-
-
Schilling, O.1
Auf dem Keller, U.2
Overall, C.M.3
-
29
-
-
78651069641
-
Characterization of the prime and non-prime active site specificities of proteases by proteome-derived peptide libraries and tandem mass spectrometry
-
Schilling O., Huesgen P.F., Barré O., Auf dem Keller U., Overall C.M. Characterization of the prime and non-prime active site specificities of proteases by proteome-derived peptide libraries and tandem mass spectrometry. Nat. Protoc. 2011, 6:111-120. 10.1038/nprot.2010.178.
-
(2011)
Nat. Protoc.
, vol.6
, pp. 111-120
-
-
Schilling, O.1
Huesgen, P.F.2
Barré, O.3
Auf dem Keller, U.4
Overall, C.M.5
-
30
-
-
44949142150
-
Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites
-
Schilling O., Overall C.M. Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat. Biotechnol. 2008, 26:685-694. 10.1038/nbt1408.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 685-694
-
-
Schilling, O.1
Overall, C.M.2
-
31
-
-
84890928051
-
Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity
-
Marino G., Huesgen P.F., Eckhard U., Overall C.M., Schröder W.P., Funk C. Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity. Biochem. J. 2014, 457:335-346. 10.1042/BJ20130196.
-
(2014)
Biochem. J.
, vol.457
, pp. 335-346
-
-
Marino, G.1
Huesgen, P.F.2
Eckhard, U.3
Overall, C.M.4
Schröder, W.P.5
Funk, C.6
-
32
-
-
84897038767
-
Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen
-
Eckhard U., Huesgen P.F., Brandstetter H., Overall C.M. Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen. J. Proteomics 2014, 100:102-114. 10.1016/j.jprot.2013.10.004.
-
(2014)
J. Proteomics
, vol.100
, pp. 102-114
-
-
Eckhard, U.1
Huesgen, P.F.2
Brandstetter, H.3
Overall, C.M.4
-
33
-
-
84907484027
-
Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs) using PICS with proteome-derived peptide libraries
-
Barré O., Dufour A., Eckhard U., Kappelhoff R., Béliveau F., Leduc R., et al. Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs) using PICS with proteome-derived peptide libraries. PLoS One 2014, 9:e105984. 10.1371/journal.pone.0105984.
-
(2014)
PLoS One
, vol.9
, pp. e105984
-
-
Barré, O.1
Dufour, A.2
Eckhard, U.3
Kappelhoff, R.4
Béliveau, F.5
Leduc, R.6
-
34
-
-
84869383618
-
CLIPPER: an add-on to the Trans-Proteomic Pipeline for the automated analysis of TAILS N-terminomics data
-
auf dem Keller U., Overall C.M. CLIPPER: an add-on to the Trans-Proteomic Pipeline for the automated analysis of TAILS N-terminomics data. Biol. Chem. 2012, 393:1477-1483. 10.1515/hsz-2012-0269.
-
(2012)
Biol. Chem.
, vol.393
, pp. 1477-1483
-
-
auf dem Keller, U.1
Overall, C.M.2
-
35
-
-
77950366024
-
Analysis of the degradome with the CLIP-CHIP microarray
-
Kappelhoff R., Auf dem Keller U., Overall C.M. Analysis of the degradome with the CLIP-CHIP microarray. Methods Mol. Biol. 2010, 622:175-193. 10.1007/978-1-60327-299-5_10.
-
(2010)
Methods Mol. Biol.
, vol.622
, pp. 175-193
-
-
Kappelhoff, R.1
Auf dem Keller, U.2
Overall, C.M.3
-
36
-
-
84925027070
-
LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification
-
Huesgen P.F., Lange P.F., Rogers L.D., Solis N., Eckhard U., Kleifeld O., et al. LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification. Nat. Methods 2015, 12:55-58. 10.1038/nmeth.3177.
-
(2015)
Nat. Methods
, vol.12
, pp. 55-58
-
-
Huesgen, P.F.1
Lange, P.F.2
Rogers, L.D.3
Solis, N.4
Eckhard, U.5
Kleifeld, O.6
-
37
-
-
84937245669
-
Proteomics beyond trypsin
-
Tsiatsiani L., Heck A.J.R. Proteomics beyond trypsin. FEBS J. 2015, 282:2612-2626. 10.1111/febs.13287.
-
(2015)
FEBS J.
, vol.282
, pp. 2612-2626
-
-
Tsiatsiani, L.1
Heck, A.J.R.2
-
38
-
-
84901945789
-
Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics
-
Guo X., Trudgian D.C., Lemoff A., Yadavalli S., Mirzaei H. Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. Mol. Cell. Proteomics 2014, 13:1573-1584. 10.1074/mcp.M113.035170.
-
(2014)
Mol. Cell. Proteomics
, vol.13
, pp. 1573-1584
-
-
Guo, X.1
Trudgian, D.C.2
Lemoff, A.3
Yadavalli, S.4
Mirzaei, H.5
-
39
-
-
84868327851
-
Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion
-
Glatter T., Ludwig C., Ahrné E., Aebersold R., Heck A.J.R., Schmidt A. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J. Proteome Res. 2012, 11:5145-5156. 10.1021/pr300273g.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 5145-5156
-
-
Glatter, T.1
Ludwig, C.2
Ahrné, E.3
Aebersold, R.4
Heck, A.J.R.5
Schmidt, A.6
-
40
-
-
0021355340
-
A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids
-
Wessel D., Flügge U.I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 1984, 138:141-143.
-
(1984)
Anal. Biochem.
, vol.138
, pp. 141-143
-
-
Wessel, D.1
Flügge, U.I.2
-
41
-
-
34548183872
-
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
-
Rappsilber J., Mann M., Ishihama Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2007, 2:1896-1906. 10.1038/nprot.2007.261.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 1896-1906
-
-
Rappsilber, J.1
Mann, M.2
Ishihama, Y.3
-
42
-
-
84867345063
-
A cross-platform toolkit for mass spectrometry and proteomics
-
Chambers M.C., Maclean B., Burke R., Amodei D., Ruderman D.L., Neumann S., et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30:918-920. 10.1038/nbt.2377.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 918-920
-
-
Chambers, M.C.1
Maclean, B.2
Burke, R.3
Amodei, D.4
Ruderman, D.L.5
Neumann, S.6
-
43
-
-
84874083265
-
NeXtProt: organizing protein knowledge in the context of human proteome projects
-
Gaudet P., Argoud-Puy G., Cusin I., Duek P., Evalet O., Gateau A., et al. neXtProt: organizing protein knowledge in the context of human proteome projects. J. Proteome Res. 2013, 12:293-298. 10.1021/pr300830v.
-
(2013)
J. Proteome Res.
, vol.12
, pp. 293-298
-
-
Gaudet, P.1
Argoud-Puy, G.2
Cusin, I.3
Duek, P.4
Evalet, O.5
Gateau, A.6
|