forked from exaexa/better-mff-thesis
-
Notifications
You must be signed in to change notification settings - Fork 0
/
refs.bib
938 lines (888 loc) · 32.9 KB
/
refs.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
@article{olsen2004trypsin,
title = {Trypsin cleaves exclusively C-terminal to arginine and lysine residues},
author = {Olsen, Jesper V and Ong, Shao-En and Mann, Matthias},
journal = {Molecular \& cellular proteomics},
volume = {3},
number = {6},
pages = {608--614},
year = {2004},
publisher = {ASBMB}
}
@article{osguthorpe2000ab,
title = {Ab initio protein folding},
author = {Osguthorpe, David J},
journal = {Current Opinion in Structural Biology},
volume = {10},
number = {2},
pages = {146--152},
year = {2000},
publisher = {Elsevier}
}
@article{hung2007collision,
title = {Collision-induced reporter fragmentations for identification of covalently modified peptides},
author = {Hung, Chien-Wen and Schlosser, Andreas and Wei, Junhua and Lehmann, Wolf D},
journal = {Analytical and bioanalytical chemistry},
volume = {389},
number = {4},
pages = {1003--1016},
year = {2007},
publisher = {Springer}
}
@article{chiu2019allosteric,
title = {Allosteric disulfides: Sophisticated molecular structures enabling flexible protein regulation},
author = {Chiu, Joyce and Hogg, Philip J},
journal = {Journal of Biological Chemistry},
volume = {294},
number = {8},
pages = {2949--5908},
year = {2019},
publisher = {ASBMB}
}
@article{mcauley2008contributions,
title = {Contributions of a disulfide bond to the structure, stability, and dimerization of human IgG1 antibody CH3 domain},
author = {Mcauley, Arnold and Jacob, Jaby and Kolvenbach, Carl G and Westland, Kimberly and Lee, Hyo Jin and Brych, Stephen R and Rehder, Douglas and Kleemann, Gerd R and Brems, David N and Matsumura, Masazumi},
journal = {Protein Science},
volume = {17},
number = {1},
pages = {95--106},
year = {2008},
publisher = {Wiley Online Library}
}
@article{brodie2017solving,
title = {Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations},
author = {Brodie, Nicholas I and Popov, Konstantin I and Petrotchenko, Evgeniy V and Dokholyan, Nikolay V and Borchers, Christoph H},
journal = {Science advances},
volume = {3},
number = {7},
pages = {e1700479},
year = {2017},
publisher = {American Association for the Advancement of Science}
}
@article{cook2013post,
title = {Post-translational control of protein function by disulfide bond cleavage},
author = {Cook, Kristina M and Hogg, Philip J},
journal = {Antioxidants \& redox signaling},
volume = {18},
number = {15},
pages = {1987--2015},
year = {2013},
publisher = {Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}
@article{nagahara2011intermolecular,
title = {Intermolecular disulfide bond to modulate protein function as a redox-sensing switch},
author = {Nagahara, N},
journal = {Amino acids},
volume = {41},
number = {1},
pages = {59--72},
year = {2011},
publisher = {Springer}
}
@article{anfinsen1973principles,
issn = {00368075, 10959203},
url = {http://www.jstor.org/stable/1736447},
author = {Christian B. Anfinsen},
journal = {Science},
number = {4096},
pages = {223--230},
publisher = {American Association for the Advancement of Science},
title = {Principles that Govern the Folding of Protein Chains},
volume = {181},
year = {1973}
}
@article{seibert2005reproducible,
title = {Reproducible polypeptide folding and structure prediction using molecular dynamics simulations},
author = {Seibert, M Marvin and Patriksson, Alexandra and Hess, Berk and Van Der Spoel, David},
journal = {Journal of molecular biology},
volume = {354},
number = {1},
pages = {173--183},
year = {2005},
publisher = {Elsevier}
}
@article{orengo1999protein,
title = {From protein structure to function},
author = {Orengo, Christine A and Todd, Annabel E and Thornton, Janet M},
journal = {Current opinion in structural biology},
volume = {9},
number = {3},
pages = {374--382},
year = {1999},
publisher = {Elsevier}
}
@article{yamin2008amyloid,
title = {Amyloid $\beta$-protein assembly as a therapeutic target of Alzheimer's disease},
author = {Yamin, Ghiam and Ono, Kenjiro and Inayathullah, Mohammed and Teplow, David B},
journal = {Current pharmaceutical design},
volume = {14},
number = {30},
pages = {3231--3246},
year = {2008},
publisher = {Bentham Science Publishers}
}
@article{konopatskaya2010protein,
title = {Protein kinase C$\alpha$: disease regulator and therapeutic target},
author = {Konopatskaya, Olga and Poole, Alastair W},
journal = {Trends in pharmacological sciences},
volume = {31},
number = {1},
pages = {8--14},
year = {2010},
publisher = {Elsevier}
}
@article{elston1998energy,
title = {Energy transduction in ATP synthase},
author = {Elston, Timothy and Wang, Hongyun and Oster, George},
journal = {Nature},
volume = {391},
number = {6666},
pages = {510--513},
year = {1998},
publisher = {Nature Publishing Group}
}
@article{ketelaar2004actin,
title = {The actin-interacting protein AIP1 is essential for actin organization and plant development},
author = {Ketelaar, Tijs and Allwood, Ellen G and Anthony, Richard and Voigt, Boris and Menzel, Diedrik and Hussey, Patrick J},
journal = {Current Biology},
volume = {14},
number = {2},
pages = {145--149},
year = {2004},
publisher = {Elsevier}
}
@article{prescott1968regulation,
title = {Regulation of cell reproduction},
author = {Prescott, David M},
journal = {Cancer Research},
volume = {28},
number = {9},
pages = {1815--1820},
year = {1968},
publisher = {American Association for Cancer Research}
}
@article{wu1997novel,
title = {A novel methodology for assignment of disulfide bond pairings in proteins},
author = {Wu, Jiang and Watson, J Throck},
journal = {Protein science},
volume = {6},
number = {2},
pages = {391--398},
year = {1997},
publisher = {Wiley Online Library}
}
@article{wedemeyer2000disulfide,
title = {Disulfide bonds and protein folding},
author = {Wedemeyer, William J and Welker, Ervin and Narayan, Mahesh and Scheraga, Harold A},
journal = {Biochemistry},
volume = {39},
number = {15},
pages = {4207--4216},
year = {2000},
publisher = {ACS Publications}
}
@article{gershon2014cleaved,
title = {Cleaved and missed sites for trypsin, Lys-C, and Lys-N can be predicted with high confidence on the basis of sequence context},
author = {Gershon, Paul D},
journal = {Journal of proteome research},
volume = {13},
number = {2},
pages = {702--709},
year = {2014},
publisher = {ACS Publications}
}
@article{kim2014ms,
title = {MS-GF+ makes progress towards a universal database search tool for proteomics},
author = {Kim, Sangtae and Pevzner, Pavel A},
journal = {Nature communications},
volume = {5},
number = {1},
pages = {1--10},
year = {2014},
publisher = {Nature Publishing Group}
}
@article{gorman2002protein,
title = {Protein disulfide bond determination by mass spectrometry},
author = {Gorman, Jeffrey J and Wallis, Tristan P and Pitt, James J},
journal = {Mass spectrometry reviews},
volume = {21},
number = {3},
pages = {183--216},
year = {2002},
publisher = {Wiley Online Library}
}
@article{smith1985design,
title = {The design of divide and conquer algorithms},
author = {Smith, Douglas R},
journal = {Science of Computer Programming},
volume = {5},
pages = {37--58},
year = {1985},
publisher = {Elsevier}
}
@book{matthiesen2007mass,
title = {Mass spectrometry data analysis in proteomics},
author = {Matthiesen, Rune and others},
volume = {367},
year = {2007},
publisher = {Springer}
}
@article{o1975high,
title = {High resolution two-dimensional electrophoresis of proteins.},
author = {O'Farrell, Patrick H},
journal = {Journal of biological chemistry},
volume = {250},
number = {10},
pages = {4007--4021},
year = {1975},
publisher = {Elsevier}
}
@article{klose1995two,
title = {Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome},
author = {Klose, Joachim and Kobalz, Ursula},
journal = {Electrophoresis},
volume = {16},
number = {1},
pages = {1034--1059},
year = {1995},
publisher = {Wiley Online Library}
}
@article{patton2002two,
title = {Two-dimensional gel electrophoresis; better than a poke in the ICAT?},
author = {Patton, Wayne F and Schulenberg, Birte and Steinberg, Thomas H},
journal = {Current opinion in biotechnology},
volume = {13},
number = {4},
pages = {321--328},
year = {2002},
publisher = {Elsevier}
}
@article{frohlich2006proteome,
title = {Proteome research based on modern liquid chromatography--tandem mass spectrometry: separation, identification and quantification},
author = {Fr{\"o}hlich, T and Arnold, GJ},
journal = {Journal of Neural Transmission},
volume = {113},
number = {8},
pages = {973--994},
year = {2006},
publisher = {Springer}
}
@article{washburn2001large,
title = {Large-scale analysis of the yeast proteome by multidimensional protein identification technology},
author = {Washburn, Michael P and Wolters, Dirk and Yates, John R},
journal = {Nature biotechnology},
volume = {19},
number = {3},
pages = {242--247},
year = {2001},
publisher = {Nature Publishing Group}
}
@book{snyder2011introduction,
title = {Introduction to modern liquid chromatography},
author = {Snyder, Lloyd R and Kirkland, Joseph J and Dolan, John W},
year = {2011},
publisher = {John Wiley \& Sons}
}
@article{chang1976high,
title = {High-performance liquid chromatography of proteins},
author = {Chang, Shung Ho and Gooding, Karen M and Regnier, Fred E},
journal = {Journal of Chromatography A},
volume = {125},
number = {1},
pages = {103--114},
year = {1976},
publisher = {Elsevier}
}
@article{mormann2008fragmentation,
title = {Fragmentation of intra-peptide and inter-peptide disulfide bonds of proteolytic peptides by nanoESI collision-induced dissociation},
author = {Mormann, Michael and Eble, Johannes and Schw{\"o}ppe, Christian and Mesters, Rolf M and Berdel, Wolfgang E and Peter-Katalini{\'c}, Jasna and Pohlentz, Gottfried},
journal = {Analytical and bioanalytical chemistry},
volume = {392},
number = {5},
pages = {831--838},
year = {2008},
publisher = {Springer}
}
@article{collins2003human,
title = {The Human Genome Project: lessons from large-scale biology},
author = {Collins, Francis S and Morgan, Michael and Patrinos, Aristides},
journal = {Science},
volume = {300},
number = {5617},
pages = {286--290},
year = {2003},
publisher = {American Association for the Advancement of Science}
}
@article{fenn1989electrospray,
title = {Electrospray ionization for mass spectrometry of large biomolecules},
author = {Fenn, John B and Mann, Matthias and Meng, Chin Kai and Wong, Shek Fu and Whitehouse, Craig M},
journal = {Science},
volume = {246},
number = {4926},
pages = {64--71},
year = {1989},
publisher = {American Association for the Advancement of Science}
}
@book{gross2006mass,
title = {Mass spectrometry: a textbook},
author = {Gross, J{\"u}rgen H},
year = {2006},
publisher = {Springer Science \& Business Media}
}
@book{field2013electron,
title = {Electron impact phenomena: and the properties of gaseous ions},
author = {Field, Frank Henry and Franklin, Joseph Louis},
volume = {1},
year = {2013},
publisher = {Academic Press}
}
@article{caprioli1997molecular,
title = {Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS},
author = {Caprioli, Richard M and Farmer, Terry B and Gile, Jocelyn},
journal = {Analytical chemistry},
volume = {69},
number = {23},
pages = {4751--4760},
year = {1997},
publisher = {ACS Publications}
}
@article{ross1997discrimination,
title = {Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry},
author = {Ross, Philip L and Lee, Katherine and Belgrader, Phillip},
journal = {Analytical Chemistry},
volume = {69},
number = {20},
pages = {4197--4202},
year = {1997},
publisher = {ACS Publications}
}
@article{clark2011collision,
title = {Collision induced dissociation products of disulfide-bonded peptides: ions result from the cleavage of more than one bond},
author = {Clark, Daniel F and Go, Eden P and Toumi, Melinda L and Desaire, Heather},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {22},
number = {3},
pages = {492--498},
year = {2011},
publisher = {ACS Publications}
}
@article{karas1985influence,
title = {Influence of the wavelength in high-irradiance ultraviolet laser desorption mass spectrometry of organic molecules},
author = {Karas, Michael and Bachmann, Doris and Hillenkamp, Franz},
journal = {Analytical chemistry},
volume = {57},
number = {14},
pages = {2935--2939},
year = {1985},
publisher = {ACS Publications}
}
@article{tsai2013mass,
title = {Mass spectrometry-based strategies for protein disulfide bond identification},
author = {Tsai, Pei Lun and Chen, Sung-Fang and Huang, Sheng Yu},
journal = {Reviews in Analytical Chemistry},
volume = {32},
number = {4},
pages = {257--268},
year = {2013},
publisher = {De Gruyter}
}
@article{wei2020identification,
title = {Identification of sulfenylated cysteines in Arabidopsis thaliana proteins using a disulfide-linked peptide reporter},
author = {Wei, Bo and Willems, Patrick and Huang, Jingjing and Tian, Caiping and Yang, Jing and Messens, Joris and Van Breusegem, Frank},
journal = {Frontiers in plant science},
volume = {11},
pages = {777},
year = {2020},
publisher = {Frontiers}
}
@inproceedings{abboud2013exact,
title = {Exact weight subgraphs and the k-sum conjecture},
author = {Abboud, Amir and Lewi, Kevin},
booktitle = {International Colloquium on Automata, Languages, and Programming},
pages = {1--12},
year = {2013},
organization = {Springer}
}
@article{li2013disulfide,
title = {Disulfide bond assignment of an IgG1 monoclonal antibody by LC--MS with post-column partial reduction},
author = {Li, Xiaojuan and Wang, Fengqiang and Xu, Wei and May, Kimberly and Richardson, Daisy and Liu, Hongcheng},
journal = {Analytical biochemistry},
volume = {436},
number = {2},
pages = {93--100},
year = {2013},
publisher = {Elsevier}
}
@article{kuratowski1930probleme,
title = {Sur le probleme des courbes gauches en topologie},
author = {Kuratowski, Kazimierz},
journal = {Fundamenta mathematicae},
volume = {15},
number = {1},
pages = {271--283},
year = {1930},
publisher = {Institute of Mathematics Polish Academy of Sciences}
}
@article{sung2016evaluation,
title = {Evaluation of disulfide scrambling during the enzymatic digestion of bevacizumab at various pH values using mass spectrometry},
author = {Sung, Wang-Chou and Chang, Chiung-Wen and Huang, Sheng-Yu and Wei, Ting-Yu and Huang, Yi-Li and Lin, Yu-Hua and Chen, Han-Min and Chen, Sung-Fang},
journal = {Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics},
volume = {1864},
number = {9},
pages = {1188--1194},
year = {2016},
publisher = {Elsevier}
}
@article{liu2014facilitating,
title = {Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS},
author = {Liu, Fan and van Breukelen, Bas and Heck, Albert JR},
journal = {Molecular \& Cellular Proteomics},
volume = {13},
number = {10},
pages = {2776--2786},
year = {2014},
publisher = {ASBMB}
}
@article{hochbaum1994node,
title = {Node-optimal connected k-subgraphs},
author = {Hochbaum, Dorit S and Pathria, Anu},
journal = {manuscript, UC Berkeley},
year = {1994}
}
@article{iglesias2010identification,
title = {Identification of cross-linked peptides by high-resolution precursor ion scan},
author = {Iglesias, Amadeu H and Santos, Luiz Fernando A and Gozzo, Fabio C},
journal = {Analytical chemistry},
volume = {82},
number = {3},
pages = {909--916},
year = {2010},
publisher = {ACS Publications}
}
@article{cui2019comprehensive,
title = {Comprehensive identification of protein disulfide bonds with pepsin/trypsin digestion, Orbitrap HCD and Spectrum Identification Machine},
author = {Cui, Chuanlong and Liu, Tong and Chen, Tong and Lu, Johanna and Casaren, Ian and Lima, Diogo Borges and Carvalho, Paulo Costa and Beuve, Annie and Li, Hong},
journal = {Journal of proteomics},
volume = {198},
pages = {78--86},
year = {2019},
publisher = {Elsevier}
}
@article{opiteck1997comprehensive,
title = {Comprehensive on-line LC/LC/MS of proteins},
author = {Opiteck, Gregory J and Lewis, Kenneth C and Jorgenson, James W and Anderegg, Robert J},
journal = {Analytical chemistry},
volume = {69},
number = {8},
pages = {1518--1524},
year = {1997},
publisher = {ACS Publications}
}
@article{johnson1994sequential,
title = {Sequential protein kinase reactions controlling cell growth and differentiation},
author = {Johnson, Gary L and Vaillancourt, Richard R},
journal = {Current opinion in cell biology},
volume = {6},
number = {2},
pages = {230--238},
year = {1994},
publisher = {Elsevier}
}
@article{dole1968molecular,
title = {Molecular beams of macroions},
author = {Dole, Malcolm and Mack, Lawrence L and Hines, Robert L and Mobley, Ralph C and Ferguson, Lowell D and Alice, Martin B},
journal = {The Journal of chemical physics},
volume = {49},
number = {5},
pages = {2240--2249},
year = {1968},
publisher = {American Institute of Physics}
}
@article{dole1968gas,
title = {Gas phase macroions},
author = {Dole, Malcolm and Hines, RL and Mack, LL and Mobley, RC and Ferguson, LD and Alice, MB},
journal = {Macromolecules},
volume = {1},
number = {1},
pages = {96--97},
year = {1968},
publisher = {ACS Publications}
}
@article{fenn1990electrospray,
title = {Electrospray ionization--principles and practice},
author = {Fenn, John B and Mann, Matthias and Meng, Chin Kai and Wong, Shek Fu and Whitehouse, Craige M},
journal = {Mass Spectrometry Reviews},
volume = {9},
number = {1},
pages = {37--70},
year = {1990},
publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken}
}
@article{rayleigh1882xx,
title = {XX. On the equilibrium of liquid conducting masses charged with electricity},
author = {Rayleigh, Lord},
journal = {The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science},
volume = {14},
number = {87},
pages = {184--186},
year = {1882},
publisher = {Taylor \& Francis}
}
@article{lima2015sim,
title = {SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis},
author = {Lima, Diogo B and de Lima, Tatiani B and Balbuena, Tiago S and Neves-Ferreira, Ana Gisele C and Barbosa, Valmir C and Gozzo, F{\'a}bio C and Carvalho, Paulo C},
journal = {Journal of proteomics},
volume = {129},
pages = {51--55},
year = {2015},
publisher = {Elsevier}
}
@article{boyd2007branch,
title = {Branch and bound methods},
author = {Boyd, Stephen and Mattingley, Jacob},
journal = {Notes for EE364b, Stanford University},
pages = {2006--07},
year = {2007},
publisher = {Citeseer}
}
@article{wu2009mass,
title = {Mass spectrometric determination of disulfide linkages in recombinant therapeutic proteins using online LC- MS with electron-transfer dissociation},
author = {Wu, Shiaw-Lin and Jiang, Haitao and Lu, Qiaozhen and Dai, Shujia and Hancock, William S and Karger, Barry L},
journal = {Analytical chemistry},
volume = {81},
number = {1},
pages = {112--122},
year = {2009},
publisher = {ACS Publications}
}
@article{go2011analysis,
title = {Analysis of the disulfide bond arrangement of the HIV-1 envelope protein CON-S gp140 $\Delta$CFI shows variability in the V1 and V2 regions},
author = {Go, Eden P and Zhang, Ying and Menon, Sushma and Desaire, Heather},
journal = {Journal of proteome research},
volume = {10},
number = {2},
pages = {578--591},
year = {2011},
publisher = {ACS Publications}
}
@article{lakbub2018recent,
title = {Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins},
author = {Lakbub, Jude C and Shipman, Joshua T and Desaire, Heather},
journal = {Analytical and bioanalytical chemistry},
volume = {410},
number = {10},
pages = {2467--2484},
year = {2018},
publisher = {Springer}
}
@article{durand2013tandem,
title = {Tandem mass spectrometry (MSn) of peptide disulfide regio-isomers via collision-induced dissociation: utility and limits in disulfide bond characterization},
author = {Durand, Kirt L and Ma, Xiaoxiao and Plummer, Chelsea E and Xia, Yu},
journal = {International Journal of Mass Spectrometry},
volume = {343},
pages = {50--57},
year = {2013},
publisher = {Elsevier}
}
@article{griffiths2001electrospray,
title = {Electrospray and tandem mass spectrometry in biochemistry},
author = {Griffiths, William J and JONSSON, Andreas P and LIU, Suya and RAI, Dilip K and WANG, Yuqin},
journal = {Biochemical Journal},
volume = {355},
number = {3},
pages = {545--561},
year = {2001},
publisher = {Portland Press Ltd.}
}
@article{felitsyn2002origin,
title = {Origin and number of charges observed on multiply-protonated native proteins produced by ESI},
author = {Felitsyn, Natalia and Peschke, Michael and Kebarle, Paul},
journal = {International Journal of Mass Spectrometry},
volume = {219},
number = {1},
pages = {39--62},
year = {2002},
publisher = {Elsevier}
}
@article{domon2006mass,
title = {Mass spectrometry and protein analysis},
author = {Domon, Bruno and Aebersold, Ruedi},
journal = {science},
volume = {312},
number = {5771},
pages = {212--217},
year = {2006},
publisher = {American Association for the Advancement of Science}
}
@article{stephens1946pulsed,
title = {A Pulsed Mass Spectrometer with Time Disaersion},
author = {Stephens, WE},
journal = {Phys. Rev.},
volume = {69},
pages = {691},
year = {1946}
}
@article{fuerstenau1995molecular,
title = {Molecular weight determination of megadalton DNA electrospray ions using charge detection time-of-flight mass spectrometry},
author = {Fuerstenau, Stephen D and Benner, W Henry},
journal = {Rapid Communications in Mass Spectrometry},
volume = {9},
number = {15},
pages = {1528--1538},
year = {1995},
publisher = {Wiley Online Library}
}
@article{paul1990electromagnetic,
title = {Electromagnetic traps for charged and neutral particles (Nobel lecture)},
author = {Paul, Wolfgang},
journal = {Angewandte Chemie International Edition in English},
volume = {29},
number = {7},
pages = {739--748},
year = {1990},
publisher = {Wiley Online Library}
}
@article{paul1953neues,
title = {Ein neues massenspektrometer ohne magnetfeld},
author = {Paul, Wolfgang and Steinwedel, Helmut},
journal = {Zeitschrift f{\"u}r Naturforschung A},
volume = {8},
number = {7},
pages = {448--450},
year = {1953},
publisher = {Verlag der Zeitschrift f{\"u}r Naturforschung}
}
@article{yost1978selected,
title = {Selected ion fragmentation with a tandem quadrupole mass spectrometer},
author = {Yost, RA and Enke, CG},
journal = {Journal of the American Chemical Society},
volume = {100},
number = {7},
pages = {2274--2275},
year = {1978},
publisher = {ACS Publications}
}
@misc{2021Mass,
title = {Mass Analyzers (Mass Spectrometry)},
url = {https://chem.libretexts.org/@go/page/324},
note = {[Online; accessed 2021-08-03]},
date = {2021-05-18},
year = 2021,
month = 5,
day = 18
}
@article{mao2003h,
title = {H/D exchange of gas phase bradykinin ions in a linear quadrupole ion trap},
author = {Mao, Dunmin and Douglas, DJ},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {14},
number = {2},
pages = {85--94},
year = {2003},
publisher = {ACS Publications}
}
@article{lawrence1932production,
title = {The production of high speed light ions without the use of high voltages},
author = {Lawrence, Ernest O and Livingston, M Stanley},
journal = {Physical Review},
volume = {40},
number = {1},
pages = {19},
year = {1932},
publisher = {APS}
}
@article{comisarow1974fourier,
title = {Fourier transform ion cyclotron resonance spectroscopy},
author = {Comisarow, Melvin B and Marshall, Alan G},
journal = {Chemical physics letters},
volume = {25},
number = {2},
pages = {282--283},
year = {1974},
publisher = {Elsevier}
}
@article{easterling1999routine,
title = {Routine part-per-million mass accuracy for high-mass ions: Space-charge effects in MALDI FT-ICR},
author = {Easterling, Michael L and Mize, Todd H and Amster, I Jonathan},
journal = {Analytical chemistry},
volume = {71},
number = {3},
pages = {624--632},
year = {1999},
publisher = {ACS Publications}
}
@article{amster1996fourier,
title = {Fourier transform mass spectrometry},
author = {Amster, I Jonathan},
journal = {Journal of mass spectrometry},
volume = {31},
number = {12},
pages = {1325--1337},
year = {1996},
publisher = {Wiley Online Library}
}
@article{hu2005orbitrap,
title = {The Orbitrap: a new mass spectrometer},
author = {Hu, Qizhi and Noll, Robert J and Li, Hongyan and Makarov, Alexander and Hardman, Mark and Graham Cooks, R},
journal = {Journal of mass spectrometry},
volume = {40},
number = {4},
pages = {430--443},
year = {2005},
publisher = {Wiley Online Library}
}
@article{zubarev2000electron,
title = {Electron capture dissociation for structural characterization of multiply charged protein cations},
author = {Zubarev, Roman A and Horn, David M and Fridriksson, Einar K and Kelleher, Neil L and Kruger, Nathan A and Lewis, Mark A and Carpenter, Barry K and McLafferty, Fred W},
journal = {Analytical chemistry},
volume = {72},
number = {3},
pages = {563--573},
year = {2000},
publisher = {ACS Publications}
}
@article{syka2004peptide,
title = {Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry},
author = {Syka, John EP and Coon, Joshua J and Schroeder, Melanie J and Shabanowitz, Jeffrey and Hunt, Donald F},
journal = {Proceedings of the National Academy of Sciences},
volume = {101},
number = {26},
pages = {9528--9533},
year = {2004},
publisher = {National Acad Sciences}
}
@article{hart2014review,
title = {A review of electron-capture and electron-transfer dissociation tandem mass spectrometry in polymer chemistry},
author = {Hart-Smith, Gene},
journal = {Analytica chimica acta},
volume = {808},
pages = {44--55},
year = {2014},
publisher = {Elsevier}
}
@article{oomens2006gas,
title = {Gas-phase infrared multiple photon dissociation spectroscopy of mass-selected molecular ions},
author = {Oomens, Jos and Sartakov, Boris G and Meijer, Gerard and Von Helden, Gert},
journal = {International Journal of Mass Spectrometry},
volume = {254},
number = {1-2},
pages = {1--19},
year = {2006},
publisher = {Elsevier}
}
@incollection{matthiesen2013introduction,
title = {Introduction to mass spectrometry-based proteomics},
author = {Matthiesen, Rune and Bunkenborg, Jakob},
booktitle = {Mass spectrometry data analysis in proteomics},
pages = {1--45},
year = {2013},
publisher = {Springer}
}
@article{quan2013cid,
title = {CID, ETD and HCD fragmentation to study protein post-translational modifications},
author = {Quan, Lingdong and Liu, Miao},
journal = {Mod Chem Appl},
volume = {1},
number = {1},
pages = {1--5},
year = {2013}
}
@article{xia2006ion,
title = {Ion trap versus low-energy beam-type collision-induced dissociation of protonated ubiquitin ions},
author = {Xia, Yu and Liang, Xiaorong and McLuckey, Scott A},
journal = {Analytical chemistry},
volume = {78},
number = {4},
pages = {1218--1227},
year = {2006},
publisher = {ACS Publications}
}
@article{olsen2007higher,
title = {Higher-energy C-trap dissociation for peptide modification analysis},
author = {Olsen, Jesper V and Macek, Boris and Lange, Oliver and Makarov, Alexander and Horning, Stevan and Mann, Matthias},
journal = {Nature methods},
volume = {4},
number = {9},
pages = {709--712},
year = {2007},
publisher = {Nature Publishing Group}
}
@article{michalski2012systematic,
title = {A systematic investigation into the nature of tryptic HCD spectra},
author = {Michalski, Annette and Neuhauser, Nadin and Cox, Jürgen and Mann, Matthias},
journal = {Journal of proteome research},
volume = {11},
number = {11},
pages = {5479--5491},
year = {2012},
publisher = {ACS Publications}
}
@article{louris1987instrumentation,
title = {Instrumentation, applications, and energy deposition in quadrupole ion-trap tandem mass spectrometry},
author = {Louris, John N and Cooks, R Graham and Syka, John EP and Kelley, Paul E and Stafford, George C and Todd, John FJ},
journal = {Analytical Chemistry},
volume = {59},
number = {13},
pages = {1677--1685},
year = {1987},
publisher = {ACS Publications}
}
@article{katta1991use,
title = {Use of a single-quadrupole mass spectrometer for collision-induced dissociation studies of multiply charged peptide ions produced by electrospray ionization},
author = {Katta, Viswanatham and Chowdhury, Swapan K and Chait, Brian T},
journal = {Analytical chemistry},
volume = {63},
number = {2},
pages = {174--178},
year = {1991},
publisher = {ACS Publications}
}
@article{paizs2005fragmentation,
title = {Fragmentation pathways of protonated peptides},
author = {Paizs, B{\'e}la and Suhai, S{\'a}ndor},
journal = {Mass spectrometry reviews},
volume = {24},
number = {4},
pages = {508--548},
year = {2005},
publisher = {Wiley Online Library}
}
@article{giese2016study,
title = {A study into the collision-induced dissociation (CID) behavior of cross-linked peptides},
author = {Giese, Sven H and Fischer, Lutz and Rappsilber, Juri},
journal = {Molecular \& Cellular Proteomics},
volume = {15},
number = {3},
pages = {1094--1104},
year = {2016},
publisher = {ASBMB}
}
@article{lioe2007novel,
title = {A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation},
author = {Lioe, Hadi and OrsHair, Richard AJ},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {18},
number = {6},
pages = {1109--1123},
year = {2007},
publisher = {ACS Publications}
}
@article{bean1992characterization,
title = {Characterization of disulfide bond position in proteins and sequence analysis of cystine-bridged peptides by tandem mass spectrometry},
author = {Bean, Mark F and Carr, Steven A},
journal = {Analytical biochemistry},
volume = {201},
number = {2},
pages = {216--226},
year = {1992},
publisher = {Elsevier}
}
@article{zhang2006mapping,
title = {Mapping of protein disulfide bonds using negative ion fragmentation with a broadband precursor selection},
author = {Zhang, Mingxuan and Kaltashov, Igor A},
journal = {Analytical chemistry},
volume = {78},
number = {14},
pages = {4820--4829},
year = {2006},
publisher = {ACS Publications}
}