Analysis of mixture sequences derived from edman degradation data

Henzel, William J.; Stults, John T.; Wong, Susan; Namenuk, Angela K.; Yashio, James; Watanabe, Colin

doi:10.1016/s1080-8914(96)80038-x

Cited by 5 publications

(6 citation statements)

References 6 publications

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“…At the same time, we also developed a program, called "SEQSORT", that was able to sort mixture sequences obtained from automated Edman sequencing data and was later published [7]. The program generated a matrix of sequences using all possible combinations of adjacent amino acids observed in the Edman sequence data.…”

Section: The Quest For Faster Protein Sequence Analysis 1989mentioning

confidence: 99%

“…Obtaining sufficient sequence for cDNA cloning on proteins at the low picomole amounts was still a challenge. To meet this need, we developed another program called "MOLWFIT" which utilized masses obtained from MALDI mass analysis and Edman sequence data of capillary reversed-phase separated fractions after endoprotease digestion [7]. The masses and sequences obtained were used as input for this program.…”

Section: Mass Spectrometry Evolves 1992mentioning

confidence: 99%

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Protein identification: The origins of peptide mass fingerprinting

Henzel¹,

Watanabe²,

Stults³

2003

J. Am. Soc. Mass Spectrom.

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241

157

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Peptide mass fingerprinting (PMF) grew from a need for a faster, more efficient method to identify frequently observed proteins in electrophoresis gels. We describe the genesis of the idea in 1989, and show the first demonstration with fast atom bombardment mass spectrometry. Despite its promise, the method was seldom used until 1992, with the coming of significantly more sensitive commercial instrumentation based on MALDI-TOF-MS. We recount the evolution of the method and its dependence on a number of technical breakthroughs, both in mass spectrometry and in other areas. We show how it laid the foundation for high-throughput, high-sensitivity methods of protein analysis, now known as proteomics. We conclude with recommendations for further improvements, and speculation of the role of PMF in the future. (J Am Soc Mass Spectrom 2003, 14, 931-942)

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Section: The Quest For Faster Protein Sequence Analysis 1989mentioning

confidence: 99%

Section: Mass Spectrometry Evolves 1992mentioning

confidence: 99%

Protein identification: The origins of peptide mass fingerprinting

Henzel¹,

Watanabe²,

Stults³

2003

J. Am. Soc. Mass Spectrom.

Self Cite

241

157

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“…SEQSORT. The SEQSORT algorithm was used to sort sequence mixtures. , The algorithm finds patterns specified as regular-expression syntax. Sequence mixtures can be sorted using a known sequence or by comparing the sequence mixture with all proteins in a protein sequence database.…”

Section: Methodsmentioning

confidence: 99%

High-Throughput Protein Sequencing

Pham¹,

Tropea²,

Wong³

et al. 2003

Anal. Chem.

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We have designed and implemented an autosampler that provides additional sample capacity on a commercial protein sequencer. The autosampler attaches to a standard ABI Procise sequencer, enabling a single-sample cartridge to hold up to six separate samples. The autosampler is used in combination with faster Edman cycles and a rapid 12-min PTH separation to significantly increase the speed of automated protein sequencing. We also describe Edman chemistry modifications that improve coupling efficiency and prevent internal cleavage that can occur when samples are sequenced in the standard glass cartridges.

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“…After digestion, membranes were rinsed thoroughly with water, dried and subjected to N-terminal sequencing. Due to the presence of multiple peptide sequences being generated from the proteolytic digestion, data were analyzed using the SEQ-SORT algorithm [33]. Two publicly available programs (FASTS and FASTF) for sorting multiple sequences are also available [34].…”

Section: Rapid On-membrane Digestion For Automated Edman Degradationmentioning

confidence: 99%

Rapid on-membrane proteolytic cleavage for Edman sequencing and mass spectrometric identification of proteins

Pham¹,

Henzel²,

Lill³

2005

Electrophoresis

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A method for the rapid limited enzymatic cleavage of PVDF membrane-immobilized proteins is described. This method allows the fast characterization of PVDF blotted proteins by peptide mass fingerprinting (Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., Wantanabe, C., Proc. Natl. Acad. Sci. USA 1993, 90, 5011-5015), LC-MS/MS, or N-terminal sequencing and has been demonstrated on a range of proteins using a full complement of proteolytic enzymes. This technique allows the generation of proteolytic fragments between 5 and 60 min (depending on the enzyme employed), which is significantly faster than previously reported on-membrane digestion methods. To date, this on-membrane rapid digestion protocol has aided in the identification and confirmation of mutation sites in over 200 recombinant proteins.

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Analysis of mixture sequences derived from edman degradation data

Cited by 5 publications

References 6 publications

Protein identification: The origins of peptide mass fingerprinting

Protein identification: The origins of peptide mass fingerprinting

High-Throughput Protein Sequencing

Rapid on-membrane proteolytic cleavage for Edman sequencing and mass spectrometric identification of proteins

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