-
A Synthetic Peptide for Evaluating Protein Sequencing Capabilities: Design of ABRF-93SEQ and Results. In (J.W. Crabb, ed.) Techniques in Protein Chemistry V, Academic Press, San Diego, pp133-141 (1994)
Rush, J., Andrews, P. C., Crimmins, D. L., Gambee, J. E., Grant, G. A., Mische, S. M. and Speicher, D. W.
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ABRF ESRG 2005 Study: identification of seven modified amino acids by Edman sequencing. J Biomol Tech, 2006. 17(5): p. 308-326.
Brune, D., N.D. Denslow, R. Kobayashi, W.S. Lane, J.W. Leone, B.J. Madden, J.M. Neveu, and J. Pohl
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ABRF-2002 ESRG, A Difficult Sequence: Analysis of a PVDF-Bound KNown Protein With a Heterogeneous Amino-Terminus Journal of Biomolecular Techniques 13:246-257 (2002).
Buckel, S.D., Cook,R.G., Crawford, J.M., Dupont, D.R., Madden,B.J., Neveu,J.M., Steinke, L., Fernandez, J
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ABRF-2003 ESRG: Analysis of a PVDF-Bound KNown Protein With a Heterogeneous Amino-Terminus Journal of Biomolecular Techniques 14:278-288 (2003).
Buckel, S.D., Cook,R.G., Crawford,M.J., Denslow, N., Madden,B.J., Steinke, L., Fernandez, J., Neveu,J.M
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ABRF-97SEQ: Sequencing Results of a Low-Level Sample. J Biomol Tech, 10:26-32 (1999)
Stone, K., Fernandez, J., Admon, A., Henzel, W., Lane, W., Rohde, M., and Steinke, L.
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ABRF-98SEQ: Evaluation of peptide sequencing at high sensitivity J. Biomol. Tech., Jun 2000; 11: 92 - 99.
WJ Henzel, A Admon, SA Carr, G Davis, K De Jongh, W Lane, M Rohde, and L Steinke
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Amino Acid Analysis and Sequencing - What Is State-of-the-Art?
Niece, R.L., L.H. Ericsson, A.V. Fowler, A.J. Smith, D.W. Speicher, J.W. Crabb, and K.R. Williams.
"Methods in Protein Sequence Analysis" (H. Jörnvall, J.-O. Höög, and A.-M. Gustavsson, Eds.), Birkhäuser Verlag, Basel, 133-141, 1991
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Assignment of Cysteine and Tryptophan Residues during Protein Sequencing: Results of ABRF-94SEQ. In (J. W. Crabb, ed.) Techniques in Protein Chemistry VI, Academic Press, San Diego, pp 209-217 (1995)
Gambee, J. E., Andrews, P. C., Grant, G. A., Merrill, B., Mische, S. M. and Rush, J.
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Design and Analysis of ABRF-95SEQ, a Recombinant Protein with Sequence Heterogeneity. In (D. Marshak, ed.) Techniques in Protein Chemistry VII, Academic Press, San Diego, pp 347-358 (1996)
DeJongh, K. S., Fernandez, J., Gambee, J. E., Grant, G. A., Merrill, B., Stone, K. L. and Rush, J.
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Design, Characterization and Results of ABRF-89SEQ: A Test Sample for Evaluating Protein Sequencer Performance in Protein Microchemistry Core Facilities. In (T. E. Hugli, ed.) Current Research in Protein Chemistry, Academic Press, pp 159-166 (1989)
Speicher, D. W., Grant, G. A., Niece, R. L., Blacher, R. W., Fowler A. V. and Williams, K. R.
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Edman Sequencing Research Group 2004 Study: Modified Amino Acids in Edman Sequencing, J. Biomol. Tech., Sep 2005; 16: 272 - 284.
D. Brune, J.M. Crawford, R.G. Cook, N.D. Denslow, R. Kobayashi, B.J. Madden, J. M. Neveu, and L. Steinke
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Evaluation of ABRF-96SEQ: A Sequence Assignment Exercise. In (D. R. Marshak, ed.) Techniques in Protein Chemistry VIII, Academic Press, San Diego, pp 69-78 (1997)
Fernandez, J., Admon, A., DeJongh, K., Grant, G., Henzel, W., Lane, W. S., Stone, K. L. and Merrill, B.
-
Evaluation of Protein Sequencing Core Facilities: Design, Characterization, and Results form a Test Sample (ABRF-91SEQ). In (R. H. Angeletti, ed.) Techniques in Protein Chemistry III, Academic Press, San Diego, pp 35-35 (1992)
Crimmins, D. L., Grant, G. A., Mende-Muller, L. M., Niece, R. L., Slaughter, C., Speicher, D. W. and Yuksel, K. U.
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Instrumentation Used in Protein and Nucleic Acid Resource Facilities: A Survey of Users
Beach, C.M. G.M. Hathaway, T.K. Hayes, A.J. Smith, and R.L. Niece.
ABRF News, Vol. 2.1 Supplement: 1-7, 1991
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Protein Sequencing from Polyvinylidene Difluoride Membranes: Design and Characterization of a Test Sample (ABRF-90SEQ) and Evaluation of Results. In (J. J. Villafranca, ed.) Techniques in Protein Chemistry II, Academic Press, San Diego, pp 151-162 (1991)
Yuksel, K. U., Grant, G. A., Mende-Muller, L. M., Niece, R. L., Williams, K. R. and Speicher, D. W.
-
Protein Sequencing of Post-translationally Modified Peptides and Proteins: Design, Characterization and Results of ABRF-92SEQ. In (R. H. Angeletti, ed.) Techniques in Protein Chemistry IV, Academic Press, San Diego, pp 453-461 (1993)
Mische, S. M., Yuksel, K. U., Mende-Muller, L. M., Matsudaira, P., Crimmins, D. L. and Andrews, P. C.
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in "Techniques in Protein Chemistry" (Hugli, T., Ed.), Academic Press, San Diego, 89-110, 1989
2000 ABRF Peptide Sequencing by Mass Spectrometry Quiz
Introduction
Prior to its demise, the ABRF Mass Spectrometry Committee prepared four "tryptic" peptides whose sequences did not match anything in the public nucleotide or protein sequence databases. For two of these peptides, data was acquired using an ion trap mass spectrometer, and for the other two a quadrupole / time-of-flight hybrid mass spectrometer (Qtof) was used. Using these data, a MS/MS peptide sequencing quiz was prepared for the ABRF membership, where the aim was four-fold. First, this was a sort of late final exam for those who took the 1999 ABRF course taught by Prof. Don Hunt. Second, the results might indicate the need for similar additional ABRF courses. Third, the anonymous results allowed individuals to assess their own level of proficiency at this task. Fourth, it allowed a comparison of the relative merits of two types of mass spectrometers most commonly used for peptide sequencing.
This study is closed, and the results and answers can be found here. I suppose one could still take the quiz, but you'll have to grade yourself.
The Quiz
Check out the sequencing tutorial, if you need instructions on sequencing tryptic peptides using low energy CID data.
Ion trap data
Data for two peptides was acquired, where the first one is the easiest. To aid in the verification of your proposed sequences, MS3 spectra were acquired for both peptides. The following are all standard gif files:
Qtof data
The next two problems were obtained from a quadrupole / time-of-flight hybrid mass spectrometer (Qtof), where the third peptide is easier than the fourth. The fourth peptide was also subjected to trypsin in the presence of a 1:1 mixture of 16O and 18O water, which labeled the C-terminus with a mixture of the two stable isotopes. The precursor resolution was set wide enough to pass both the 16O and 18O labeled peptide, such that C-terminal fragment ions in the MS/MS spectrum exhibited two mass unit doublets. There are two spectra shown, where the raw data is on top, and the spectrum beneath it is the same data subjected to a y-ion filter.
- ABRF MS Sequencing Problem #3 (16O only)
- ABRF MS Sequencing Problem #4 (16O only)
- ABRF MS Sequencing Problem #4 (C-terminus labeled with 16O and 18O). To view this you will need a copy of Acrobat Reader, which can be obtained from the Adobe Acrobat web site.
Synthetic Peptide for Evaluating Protein Sequencer and Amino Acid Analyzer Performance in Core Facilities: Design and Results
Niece, R.L., K.R. Williams, C.L. Wadsworth, J. Elliott, K.L. Stone, W.J. McMurray, A. Fowler, D. Atherton, R. Kutny, and A.J. Smith. A.
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