Algorithms for thede novosequencing of peptides from tandem mass spectra

Abstract

Proteomics is the study of the proteins, their time and location dependent expression profiles as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Typically database search methods are employed to identify proteins from complex mixtures. However, often databases are not available or despite their availability some sequences are not readily found therein. To overcome this problem de novo sequencing can be used to directly assign a peptide sequence to an MS/MS spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them is detailed in this review. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and finally, examples are used to construct possible future perspectives of the field. Running title:De novo sequencing of MS/MS spectra

Ranking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matches

“…One, de novo sequencing, assigns a sequence to the MS/MS spectrum with no additional information [3], while the other (database search) uses a sequence database to select the best matching peptide from a list of expected proteins. Many algorithms have been proposed for both de novo sequencing [3] and database search [4], [5]. In database search, OMSSA [6], X!Tandem [7], and MSGFDB [8] are prominent free tools.…”

Comparative Secretome Profiling and Mutant Protein Identification in Metastatic Prostate Cancer Cells by Quantitative Mass Spectrometry-based Proteomics

“…De novo sequencing algorithms can directly indicate amino acid sequence without database matching, but its accuracy is not reliable enough, mostly due to ambiguous interpretations of MS/MS spectra (13). However, database search algorithms, associated with cancer-related mutation database, such as Unknown peptidelevel Mutation Analysis (XMAn), Human Cancer Proteome Variation Database (CanProVar), and Cancer Mutation Proteome Database (CMPD), can be used to identify the relevant mutant proteins (14)(15)(16).…”

CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

“…Many tools for de novo sequencing of linear but ribosomal peptides have been proposed [13]. For example, PEAKS is one of the most widely used commercial tools [14], and Lutefisk [15] and PepNovo [16] are popular open-source tools.…”