-
1
-
-
34548396821
-
Methods, algorithms and tools in computational proteomics: A practical point of view
-
Matthiesen R (2007) Methods, algorithms and tools in computational proteomics: A practical point of view. Proteomics 7:2815-2832
-
(2007)
Proteomics
, vol.7
, pp. 2815-2832
-
-
Matthiesen, R.1
-
2
-
-
79551483264
-
Discussion on common data analysis strategies used in MS-based proteomics
-
Matthiesen R, Azevedo L, Amorim A, Carvalho AS (2011) Discussion on common data analysis strategies used in MS-based proteomics. Proteomics 11:604-619
-
(2011)
Proteomics
, vol.11
, pp. 604-619
-
-
Matthiesen, R.1
Azevedo, L.2
Amorim, A.3
Carvalho, A.S.4
-
3
-
-
0027608882
-
Use of mass spectrometric molecular weight information to identify proteins in sequence databases
-
Mann M, Hojrup P, Roepstorff P (1993) Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 22:338-345
-
(1993)
Biol Mass Spectrom
, vol.22
, pp. 338-345
-
-
Mann, M.1
Hojrup, P.2
Roepstorff, P.3
-
5
-
-
10244268784
-
A suffix tree approach to the interpretation of tandem mass spectra: Applications to peptides of non-specific digestion and post-Translational modifications
-
Lu B, Chen T (2003) A suffix tree approach to the interpretation of tandem mass spectra: Applications to peptides of non-specific digestion and post-Translational modifications. Bioinformatics 19(Suppl 2):ii113-ii121
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL.2
-
-
Lu, B.1
Chen, T.2
-
6
-
-
23944455372
-
Peptide sequence tags for fast database search in mass-spectrometry
-
Frank A, Tanner S, Bafna V, Pevzner P (2005) Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res 4:1287-1295
-
(2005)
J Proteome Res
, vol.4
, pp. 1287-1295
-
-
Frank, A.1
Tanner, S.2
Bafna, V.3
Pevzner, P.4
-
7
-
-
0345600791
-
Guten-Tag: High-Throughput sequence tagging via an empirically derived fragmentation model
-
Tabb DL, Saraf A, Yates JR III (2003) Guten-Tag: High-Throughput sequence tagging via an empirically derived fragmentation model. Anal Chem 75:6415-6421
-
(2003)
Anal Chem
, vol.75
, pp. 6415-6421
-
-
Tabb, D.L.1
Saraf, A.2
Yates III, J.R.3
-
8
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
-
9
-
-
0036807449
-
Error tolerant searching of uninterpreted tandem mass spectrometry data
-
Creasy DM, Cottrell JS (2002) Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2:1426-1434
-
(2002)
Proteomics
, vol.2
, pp. 1426-1434
-
-
Creasy, D.M.1
Cottrell, J.S.2
-
10
-
-
26844556940
-
Parallel tandem: A program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem
-
Duncan DT, Craig R, Link AJ (2005) Parallel tandem: A program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem. J Proteome Res 4:1842-1847
-
(2005)
J Proteome Res
, vol.4
, pp. 1842-1847
-
-
Duncan, D.T.1
Craig, R.2
Link, A.J.3
-
11
-
-
84855166719
-
MR-Tandem: Parallel X!Tandem using Hadoop MapReduce on Amazon Web Services
-
Pratt B, Howbert JJ, Tasman NI, Nilsson EJ (2012) MR-Tandem: Parallel X!Tandem using Hadoop MapReduce on Amazon Web Services. Bioinformatics 28:136-137
-
(2012)
Bioinformatics
, vol.28
, pp. 136-137
-
-
Pratt, B.1
Howbert, J.J.2
Tasman, N.I.3
Nilsson, E.J.4
-
12
-
-
29144535689
-
VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-Translational modifications in proteins
-
Matthiesen R, Trelle MB, Hojrup P, Bunkenborg J, Jensen ON (2005) VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-Translational modifications in proteins. J Proteome Res 4:2338-2347
-
(2005)
J Proteome Res
, vol.4
, pp. 2338-2347
-
-
Matthiesen, R.1
Trelle, M.B.2
Hojrup, P.3
Bunkenborg, J.4
Jensen, O.N.5
-
13
-
-
77951030626
-
Virtual expert mass spectrometrist: ITRAQ tool for database-dependent search, quantitation and result storage
-
Rodriguez-Suarez E, Gubb E, Alzueta IF, Falcon-Perez JM, Amorim A, Elortza F, Matthiesen R (2010) Virtual expert mass spectrometrist: ITRAQ tool for database-dependent search, quantitation and result storage. Proteomics 10:1545-1556
-
(2010)
Proteomics
, vol.10
, pp. 1545-1556
-
-
Rodriguez-Suarez, E.1
Gubb, E.2
Alzueta, I.F.3
Falcon-Perez, J.M.4
Amorim, A.5
Elortza, F.6
Matthiesen, R.7
-
14
-
-
27544511899
-
InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
-
Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V (2005) InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem 77:4626-4639
-
(2005)
Anal Chem
, vol.77
, pp. 4626-4639
-
-
Tanner, S.1
Shu, H.2
Frank, A.3
Wang, L.C.4
Zandi, E.5
Mumby, M.6
Pevzner, P.A.7
Bafna, V.8
-
15
-
-
33747170146
-
Using annotated peptide mass spectrum libraries for protein identification
-
Craig R, Cortens JC, Fenyo D, Beavis RC (2006) Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res 5:1843-1849
-
(2006)
J Proteome Res
, vol.5
, pp. 1843-1849
-
-
Craig, R.1
Cortens, J.C.2
Fenyo, D.3
Beavis, R.C.4
-
16
-
-
68049100378
-
OMSSA parser: An opensource library to parse and extract data from OMSSA MS/MS search results
-
Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L (2009) OMSSA parser: An opensource library to parse and extract data from OMSSA MS/MS search results. Proteomics 9:3772-3774
-
(2009)
Proteomics
, vol.9
, pp. 3772-3774
-
-
Barsnes, H.1
Huber, S.2
Sickmann, A.3
Eidhammer, I.4
Martens, L.5
-
17
-
-
79953701087
-
Andromeda: A peptide search engine integrated into the MaxQuant environment
-
Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011) Andromeda: A peptide search engine integrated into the MaxQuant environment. J Proteome Res 10:1794-1805
-
(2011)
J Proteome Res
, vol.10
, pp. 1794-1805
-
-
Cox, J.1
Neuhauser, N.2
Michalski, A.3
Scheltema, R.A.4
Olsen, J.V.5
Mann, M.6
-
18
-
-
0038617421
-
Volatile polydimethylcyclosiloxanes in the ambient laboratory air identified as source of extreme background signals in nanoelectrospray mass spectrometry
-
Schlosser A, Volkmer-Engert R (2003) Volatile polydimethylcyclosiloxanes in the ambient laboratory air identified as source of extreme background signals in nanoelectrospray mass spectrometry. J Mass Spectrom 38:523-525
-
(2003)
J Mass Spectrom
, vol.38
, pp. 523-525
-
-
Schlosser, A.1
Volkmer-Engert, R.2
-
19
-
-
67650725988
-
Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap
-
Cox J, Mann M (2009) Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap. J Am Soc Mass Spectrom 20:1477-1485
-
(2009)
J Am Soc Mass Spectrom
, vol.20
, pp. 1477-1485
-
-
Cox, J.1
Mann, M.2
-
20
-
-
0031298696
-
Identification of the components of simple protein mixtures by high-Accuracy peptide mass mapping and database searching
-
Jensen ON, Podtelejnikov AV, MannM(1997) Identification of the components of simple protein mixtures by high-Accuracy peptide mass mapping and database searching. Anal Chem 69:4741-4750
-
(1997)
Anal Chem
, vol.69
, pp. 4741-4750
-
-
Jensen, O.N.1
Podtelejnikov, A.V.2
Mann, M.3
-
21
-
-
0037442649
-
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
-
Fenyo D, Beavis RC (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 75:768-774
-
(2003)
Anal Chem
, vol.75
, pp. 768-774
-
-
Fenyo, D.1
Beavis, R.C.2
-
22
-
-
0043064042
-
A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases
-
Sadygov RG, Yates JR III (2003) A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem 75:3792-3798
-
(2003)
Anal Chem
, vol.75
, pp. 3792-3798
-
-
Sadygov, R.G.1
Yates III, J.R.2
-
23
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976-989
-
(1994)
J Am Soc Mass Spectrom
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates, J.R.3
-
24
-
-
0029644596
-
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
-
Yates JR III, Eng JK, McCormack AL, Schieltz D (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem 67:1426-1436
-
(1995)
Anal Chem
, vol.67
, pp. 1426-1436
-
-
Yates III, J.R.1
Eng, J.K.2
McCormack, A.L.3
Schieltz, D.4
-
25
-
-
20144365752
-
Experimental peptide identification repository (EPIR): An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data
-
Kristensen DB, Brond JC,Nielsen PA,Andersen JR, Sorensen OT, Jorgensen V, Budin K, Matthiesen J, Veno P, Jespersen HM, Ahrens CH, Schandorff S, Ruhoff PT, Wisniewski JR, Bennett KL, Podtelejnikov AV (2004) Experimental peptide identification repository (EPIR): An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data. Mol Cell Proteomics 3:1023-1038
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1023-1038
-
-
Kristensen, D.B.1
Brond, J.C.2
Nielsen, P.A.3
Andersen, J.R.4
Sorensen, O.T.5
Jorgensen, V.6
Budin, K.7
Matthiesen, J.8
Veno, P.9
Jespersen, H.M.10
Ahrens, C.H.11
Schandorff, S.12
Ruhoff, P.T.13
Wisniewski, J.R.14
Bennett, K.L.15
Podtelejnikov, A.V.16
-
26
-
-
0242653718
-
Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation
-
Kapp EA, Schutz F, Reid GE, Eddes JS, Moritz RL, O'Hair RA, Speed TP, Simpson RJ (2003) Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal Chem 75:6251-6264
-
(2003)
Anal Chem
, vol.75
, pp. 6251-6264
-
-
Kapp, E.A.1
Schutz, F.2
Reid, G.E.3
Eddes, J.S.4
Moritz, R.L.5
O'Hair, R.A.6
Speed, T.P.7
Simpson, R.J.8
-
27
-
-
20444459841
-
Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns
-
Huang Y, Triscari JM, Tseng GC, Pasa-Tolic L, Lipton MS, Smith RD, Wysocki VH (2005) Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal Chem 77:5800-5813
-
(2005)
Anal Chem
, vol.77
, pp. 5800-5813
-
-
Huang, Y.1
Triscari, J.M.2
Tseng, G.C.3
Pasa-Tolic, L.4
Lipton, M.S.5
Smith, R.D.6
Wysocki, V.H.7
-
28
-
-
27744469683
-
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 (2005) ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics 5:4096-4106
-
(2005)
Proteomics
, vol.5
, pp. 4096-4106
-
-
Zhang, N.1
Li, X.J.2
Ye, M.3
Pan, S.4
Schwikowski, B.5
Aebersold, R.6
-
29
-
-
76149113930
-
Deconvolution of mixture spectra from ion-Trap dataindependent- Acquisition tandem mass spectrometry
-
Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ (2010) Deconvolution of mixture spectra from ion-Trap dataindependent-Acquisition tandem mass spectrometry. Anal Chem 82:833-841
-
(2010)
Anal Chem
, vol.82
, pp. 833-841
-
-
Bern, M.1
Finney, G.2
Hoopmann, M.R.3
Merrihew, G.4
Toth, M.J.5
MacCoss, M.J.6
-
30
-
-
77954751922
-
Peptide identification from mixture tandem mass spectra
-
Wang J, Perez-Santiago J, Katz JE, Mallick P, Bandeira N (2010) Peptide identification from mixture tandem mass spectra. Mol Cell Proteomics 9:1476-1485
-
(2010)
Mol Cell Proteomics
, vol.9
, pp. 1476-1485
-
-
Wang, J.1
Perez-Santiago, J.2
Katz, J.E.3
Mallick, P.4
Bandeira, N.5
-
31
-
-
77955455399
-
Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies
-
Houel S, Abernathy R, Renganathan K, Meyer-Arendt K, Ahn NG, Old WM (2010) Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J Proteome Res 9:4152-4160
-
(2010)
J Proteome Res
, vol.9
, pp. 4152-4160
-
-
Houel, S.1
Abernathy, R.2
Renganathan, K.3
Meyer-Arendt, K.4
Ahn, N.G.5
Old, W.M.6
-
32
-
-
0042338362
-
A statistical model for identifying proteins by tandem mass spectrometry
-
Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75:4646-4658
-
(2003)
Anal Chem
, vol.75
, pp. 4646-4658
-
-
Nesvizhskii, A.I.1
Keller, A.2
Kolker, E.3
Aebersold, R.4
-
33
-
-
84862659627
-
SIR: Deterministic protein inference from peptides assigned to MS data
-
Matthiesen R, Prieto G, Amorim A, Aloria K, Fullaondo A, Carvalho AS, Arizmendi JM (2012) SIR: Deterministic protein inference from peptides assigned to MS data. J Proteomics 75:4176-4183
-
(2012)
J Proteomics
, vol.75
, pp. 4176-4183
-
-
Matthiesen, R.1
Prieto, G.2
Amorim, A.3
Aloria, K.4
Fullaondo, A.5
Carvalho, A.S.6
Arizmendi, J.M.7
-
34
-
-
4444249998
-
Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0
-
Matthiesen R, Bunkenborg J, Stensballe A, Jensen ON, Welinder KG, Bauw G (2004) Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics 4:2583-2593
-
(2004)
Proteomics
, vol.4
, pp. 2583-2593
-
-
Matthiesen, R.1
Bunkenborg, J.2
Stensballe, A.3
Jensen, O.N.4
Welinder, K.G.5
Bauw, G.6
-
35
-
-
65249143361
-
Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets
-
Blanco L, Mead JA, Bessant C (2009) Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets. J Proteome Res 8:1782-1791
-
(2009)
J Proteome Res
, vol.8
, pp. 1782-1791
-
-
Blanco, L.1
Mead, J.A.2
Bessant, C.3
-
36
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
Kall L, Canterbury JD, Weston J, Noble WS, MacCoss MJ (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923-925
-
(2007)
Nat Methods
, vol.4
, pp. 923-925
-
-
Kall, L.1
Canterbury, J.D.2
Weston, J.3
Noble, W.S.4
MacCoss, M.J.5
-
37
-
-
65249144535
-
A refined method to calculate false discovery rates for peptide identification using decoy databases
-
Navarro P, Vazquez J (2009) A refined method to calculate false discovery rates for peptide identification using decoy databases. J Proteome Res 8:1792-1796
-
(2009)
J Proteome Res
, vol.8
, pp. 1792-1796
-
-
Navarro, P.1
Vazquez, J.2
-
39
-
-
30744444934
-
PepHMM: A hidden Markov model based scoring function for mass spectrometry database search
-
Wany Y, Yangz A, Chen T (2006) PepHMM: A hidden Markov model based scoring function for mass spectrometry database search. Anal Chem 78:432-437
-
(2006)
Anal Chem
, vol.78
, pp. 432-437
-
-
Wany, Y.1
Yangz, A.2
Chen, T.3
-
40
-
-
70349213754
-
A Bayesian approach to protein inference problem in shotgun proteomics
-
Li YF, Arnold RJ, Li Y, Radivojac P, Sheng Q, Tang H (2009) A Bayesian approach to protein inference problem in shotgun proteomics. J Comput Biol 16:1183-1193
-
(2009)
J Comput Biol
, vol.16
, pp. 1183-1193
-
-
Li, Y.F.1
Arnold, R.J.2
Li, Y.3
Radivojac, P.4
Sheng, Q.5
Tang, H.6
-
41
-
-
84865553658
-
Data extraction from proteomics raw data: An evaluation of nine tandem MS tools using a large Orbitrap data set
-
Mancuso F, Bunkenborg J, Wierer M, Molina H (2012) Data extraction from proteomics raw data: An evaluation of nine tandem MS tools using a large Orbitrap data set. J Proteomics 75:5293-5303
-
(2012)
J Proteomics
, vol.75
, pp. 5293-5303
-
-
Mancuso, F.1
Bunkenborg, J.2
Wierer, M.3
Molina, H.4
|