De Novo Peptide Sequencing via Tandem Mass Spectrometry

Peptide sequencing via tandem mass spectrometry (MS/MS) is one of the most powerful tools in proteomics for identifying proteins. Because complete genome sequences are accumulating rapidly, the recent trend in interpretation of MS/MS spectra has been database search. However, de novo MS/MS spectral interpretation remains an open problem typically involving manual interpretation by expert mass spectrometrists. We have developed a new algorithm, SHERENGA, for de novo interpretation that automatically learns fragment ion types and intensity thresholds from a collection of test spectra generated from any type of mass spectrometer. The test data are used to construct optimal path scoring in the graph representations of MS/MS spectra. A ranked list of high scoring paths corresponds to potential peptide sequences. SHERENGA is most useful for interpreting sequences of peptides resulting from unknown proteins and for validating the results of database search algorithms in fully automated, high-throughput peptide sequencing.

[1]  N Bauman,et al.  An efficient algorithm for sequencing peptides using fast atom bombardment mass spectral data. , 1988, Biomedical & environmental mass spectrometry.

[2]  K. Ishikawa,et al.  Computer-aided peptide sequencing by fast atom bombardment mass spectrometry , 1986 .

[3]  R. Aebersold,et al.  Mass spectrometric approaches for the identification of gel‐separated proteins , 1995, Electrophoresis.

[4]  Peter R. Baker,et al.  Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. , 1999, Analytical chemistry.

[5]  Ming-Yang Kao,et al.  A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry , 2000, SODA '00.

[6]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[7]  J R Yates,et al.  Protein sequencing by tandem mass spectrometry. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Burlingame,et al.  Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra , 1992, Journal of the American Society for Mass Spectrometry.

[9]  P. Thibault,et al.  Determination of the primary structure of peptides using fast atom bombardment mass spectrometry. , 1990, Biomedical & environmental mass spectrometry.

[10]  C. Bartels.  Fast algorithm for peptide sequencing by mass spectroscopy. , 1990, Biomedical & environmental mass spectrometry.

[11]  J. Yates,et al.  The quadrupole ion trap mass spectrometer--a small solution to a big challenge. , 1997, Analytical biochemistry.

[12]  A. Shevchenko,et al.  Rapid 'de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. , 1997, Rapid communications in mass spectrometry : RCM.

[13]  M F Bean,et al.  Tandem mass spectrometry of peptides using hybrid and four-sector instruments: a comparative study. , 1991, Analytical chemistry.

[14]  Alma L. Burlingame,et al.  The Advantages and Versatility of a High-Energy Collision-Induced Dissociation-Based Strategy for the Sequence and Structural Determination of Proteins , 1994 .

[15]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[16]  A L Burlingame,et al.  Direct mass spectrometric peptide profiling and sequencing of single neurons reveals differential peptide patterns in a small neuronal network. , 1998, Biochemistry.

[17]  R S Johnson,et al.  Glutaredoxin from rabbit bone marrow. Purification, characterization, and amino acid sequence determined by tandem mass spectrometry. , 1989, The Journal of biological chemistry.

[18]  C. W. Hamm,et al.  Peptide sequencing program , 1986, Comput. Appl. Biosci..

[19]  T. Sakurai,et al.  PAAS 3: A computer program to determine probable sequence of peptides from mass spectrometric data , 1984 .

[20]  T R Hughes,et al.  Reverse transcriptase motifs in the catalytic subunit of telomerase. , 1997, Science.

[21]  S. Patterson,et al.  Proteomics: the industrialization of protein chemistry. , 2000, Current opinion in biotechnology.

[22]  A L Burlingame,et al.  Primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase determined by mass spectrometry sequence analysis and molecular cloning. Evidence for a protein motif in the sialyltransferase gene family. , 1992, The Journal of biological chemistry.

[23]  J. Villafranca,et al.  Techniques in Protein Chemistry II , 1991 .

[24]  K. Biemann.  Appendix 5. Nomenclature for peptide fragment ions (positive ions). , 1990, Methods in enzymology.

[25]  G Padron,et al.  Automated interpretation of low‐energy collision‐induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry , 2000, Electrophoresis.

[26]  B. Chait,et al.  Protein indentification using mass spectrometric information , 1998, Electrophoresis.

[27]  A. Burlingame,et al.  Peptide sequence determination by matrix-assisted laser desorption ionization employing a tandem double focusing magnetic—Orthogonal acceleration time-of-flight mass spectrometer , 1996, Journal of the American Society for Mass Spectrometry.

[28]  George Yocum,et al.  Appendix 5 , 1967 .

[29]  M. Wilm,et al.  Error-tolerant identification of peptides in sequence databases by peptide sequence tags. , 1994, Analytical chemistry.

[30]  T. Shirasawa,et al.  Differentiating alpha- and beta-aspartic acids by electrospray ionization and low-energy tandem mass spectrometry. , 2000, Rapid communications in mass spectrometry : RCM.

[31]  J. A. Taylor,et al.  Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. , 1997, Rapid communications in mass spectrometry : RCM.

[32]  K. Biemann,et al.  Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides. , 1989, Biomedical & environmental mass spectrometry.

[33]  Jorge Fernandez-de-Cossío,et al.  A computer program to aid the sequencing of peptides in collision- activated decomposition experiments , 1995, Comput. Appl. Biosci..