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In most proteome mass spectrometry experiments, more than half of the mass spectra cannot be identified, mainly because of various modifications. The open search strategy allows for a larger precursor tolerance to utilize more spectra, especially those with post-translational modifications; however, thorough quality control based on independent information is lacking. Here, we used the "Suspicious Discovery Rate (SDR)" based on translatome sequencing (RNC-seq) as an independent source to reference the proteome open search results in steady-state cells. We found that the open search strategy increased the spectra utilization with the cost of increased suspicious identifications that lack translation evidence. We further found that restricting the peptide FDR below 0.1% efficiently controlled the suspicious identifications of open search methods and thus enhanced the confidence of the peptide identification with modifications comparable to the level of the traditional narrow window search. We then demonstrated the successful and validated identification of 27 single amino acid variations from the spectra of two cell lines using the open search strategy without predefined database. These results validated the proper use of open search methods for higher-quality proteome identifications with information on post-translational modifications and single amino acid polymorphisms.
This article was published in the following journal.
Name: Journal of proteome research
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A mass spectrometry technique using two (MS/MS) or more mass analyzers. With two in tandem, the precursor ions are mass-selected by a first mass analyzer, and focused into a collision region where they are then fragmented into product ions which are then characterized by a second mass analyzer. A variety of techniques are used to separate the compounds, ionize them, and introduce them to the first mass analyzer. For example, for in GC-MS/MS, GAS CHROMATOGRAPHY-MASS SPECTROMETRY is involved in separating relatively small compounds by GAS CHROMATOGRAPHY prior to injecting them into an ionization chamber for the mass selection.
A microanalytical technique combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds.
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
A mass spectrometry technique used for analysis of nonvolatile compounds such as proteins and macromolecules. The technique involves preparing electrically charged droplets from analyte molecules dissolved in solvent. The electrically charged droplets enter a vacuum chamber where the solvent is evaporated. Evaporation of solvent reduces the droplet size, thereby increasing the coulombic repulsion within the droplet. As the charged droplets get smaller, the excess charge within them causes them to disintegrate and release analyte molecules. The volatilized analyte molecules are then analyzed by mass spectrometry.
A mass spectrometric technique that is used for the analysis of a wide range of biomolecules, such as glycoalkaloids, glycoproteins, polysaccharides, and peptides. Positive and negative fast atom bombardment spectra are recorded on a mass spectrometer fitted with an atom gun with xenon as the customary beam. The mass spectra obtained contain molecular weight recognition as well as sequence information.
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...