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CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data.
J Mass Spectrom. 2005 Apr; 40(4):475-88.JM

Abstract

We describe CHASE, a novel algorithm for automated de novo sequencing based on the mass spectrometric (MS) fragmentation analysis of tryptic peptides. This algorithm is used for protein identification from sequence similarity criteria and consists of four steps: (1) derivatization of tryptic peptides at the N-terminus with a negatively charged reagent; (2) post-source decay (PSD) fragmentation analysis of peptides; (3) interpretation of the mass peaks with the CHASE algorithm and reconstruction of the amino acid sequence; (4) transfer of these data to software for protein identifications based on sequence homology (Basic Local Alignment Search Tool, BLAST). This procedure deduced the correct amino acid sequence of tryptic peptide samples and also was able to deduce the correct sequence from difficult mass patterns and identify the amino acid sequence. This allows complete automation of the process starting from MS fragmentation of complex peptide mixtures at low concentration (e.g. from silver-stained gel bands) to identification of the protein. We also show that if PSD data are collected in a single spectrum (instead of the segmented mode offered by conventional matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrumentation), the complete workflow from MS-PSD data acquisition to similarity-based identification can be completely automated. This strategy may be applied to proteomic studies for protein identification based on automated de novo sequencing instead of MS or tandem MS patterns. We describe the Charge Assisted Sequencing Engine (CHASE) algorithm, the working protocol, the performance of the algorithm on spectra from MALDI-TOFMS and the data comparison between a TOF and a TOF-TOF instrument.

Authors+Show Affiliations

Menarini Biotech, Via Tito Speri 10, 00040 Pomezia, RM, Italy. graucci@subbiotech.itNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

15712359

Citation

Raucci, Giuseppe, et al. "CHASE, a Charge-assisted Sequencing Algorithm for Automated Homology-based Protein Identifications With Matrix-assisted Laser Desorption/ionization Time-of-flight Post-source Decay Fragmentation Data." Journal of Mass Spectrometry : JMS, vol. 40, no. 4, 2005, pp. 475-88.
Raucci G, Gabrielli M, Novelli S, et al. CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data. J Mass Spectrom. 2005;40(4):475-88.
Raucci, G., Gabrielli, M., Novelli, S., Picariello, G., & Collins, S. H. (2005). CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data. Journal of Mass Spectrometry : JMS, 40(4), 475-88.
Raucci G, et al. CHASE, a Charge-assisted Sequencing Algorithm for Automated Homology-based Protein Identifications With Matrix-assisted Laser Desorption/ionization Time-of-flight Post-source Decay Fragmentation Data. J Mass Spectrom. 2005;40(4):475-88. PubMed PMID: 15712359.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data. AU - Raucci,Giuseppe, AU - Gabrielli,Meri, AU - Novelli,Sabrina, AU - Picariello,Gianluca, AU - Collins,Stephen H, PY - 2005/2/16/pubmed PY - 2006/4/6/medline PY - 2005/2/16/entrez SP - 475 EP - 88 JF - Journal of mass spectrometry : JMS JO - J Mass Spectrom VL - 40 IS - 4 N2 - We describe CHASE, a novel algorithm for automated de novo sequencing based on the mass spectrometric (MS) fragmentation analysis of tryptic peptides. This algorithm is used for protein identification from sequence similarity criteria and consists of four steps: (1) derivatization of tryptic peptides at the N-terminus with a negatively charged reagent; (2) post-source decay (PSD) fragmentation analysis of peptides; (3) interpretation of the mass peaks with the CHASE algorithm and reconstruction of the amino acid sequence; (4) transfer of these data to software for protein identifications based on sequence homology (Basic Local Alignment Search Tool, BLAST). This procedure deduced the correct amino acid sequence of tryptic peptide samples and also was able to deduce the correct sequence from difficult mass patterns and identify the amino acid sequence. This allows complete automation of the process starting from MS fragmentation of complex peptide mixtures at low concentration (e.g. from silver-stained gel bands) to identification of the protein. We also show that if PSD data are collected in a single spectrum (instead of the segmented mode offered by conventional matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrumentation), the complete workflow from MS-PSD data acquisition to similarity-based identification can be completely automated. This strategy may be applied to proteomic studies for protein identification based on automated de novo sequencing instead of MS or tandem MS patterns. We describe the Charge Assisted Sequencing Engine (CHASE) algorithm, the working protocol, the performance of the algorithm on spectra from MALDI-TOFMS and the data comparison between a TOF and a TOF-TOF instrument. SN - 1076-5174 UR - https://www.unboundmedicine.com/medline/citation/15712359/CHASE_a_charge_assisted_sequencing_algorithm_for_automated_homology_based_protein_identifications_with_matrix_assisted_laser_desorption/ionization_time_of_flight_post_source_decay_fragmentation_data_ L2 - https://doi.org/10.1002/jms.817 DB - PRIME DP - Unbound Medicine ER -