MS-BLAST

MS-BLAST performs protein identification by conducting sequence-similarity searches using peptide sequences derived from MALDI quadrupole time-of-flight (MALDI-Q-TOF) MS/MS spectra to identify proteins from organisms lacking sequenced genomes.

Key Features:

• Integration of MALDI-Q-TOF mass spectrometry: Uses Matrix-Assisted Laser Desorption/Ionization quadrupole time-of-flight (MALDI-Q-TOF) to generate peptide mass fingerprints (PMF) and MS/MS spectra.
• Sequential database searching: Implements a multi-step search strategy beginning with peptide mass fingerprint searches, followed by searches of packets of non-interpreted MS/MS spectra, and culminating in searches using peptide sequences from automated MS/MS interpretation.
• MS BLAST homology-searching protocol: Applies a bespoke "MS BLAST" homology-search protocol tailored to accommodate limited accuracy of de novo peptide predictions.
• Automated MS/MS interpretation: Incorporates automated interpretation of MS/MS spectra to produce peptide sequences for final similarity searches.

Scientific Applications:

• Proteomics of unsequenced genomes: Identifies and characterizes proteins from organisms that lack complete genome sequences by leveraging homology matches to MS-derived peptides.
• Gel-separated protein identification: Enables identification of proteins from gel-separated bands, demonstrated by identification of 15 bands from Pichia pastoris in a proteomic study.
• Homology-based identification to mitigate de novo limits: Facilitates protein identification when de novo sequencing accuracy is limited by using homology searches on interpreted peptide sequences or packets of non-interpreted MS/MS spectra.

Methodology:

Performs sequential database searches starting with peptide mass fingerprint searches, then searches of packets of non-interpreted MS/MS spectra, and finally searches using peptide sequences obtained from automated MS/MS interpretation, applying the MS BLAST homology-searching protocol.