De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation

Abstract

De novo sequencing of peptides using tandem MS is difficult due to missing fragment ions in the spectra commonly obtained after CID of peptide precursor ions. Complementing CID spectra with spectra obtained in an ion-trap mass spectrometer upon electron transfer dissociation (ETD) significantly increases the sequence coverage with diagnostic ions. In the de novo sequencing algorithm CompNovo presented here, a divide-and-conquer approach was combined with an efficient mass decomposition algorithm to exploit the complementary information contained in CID and ETD spectra. After optimizing the parameters for the algorithm on a well-defined training data set obtained for peptides from nine known proteins, the CompNovo algorithm was applied to the de novo sequencing of peptides derived from a whole protein extract of Sorangium cellulosum bacteria. To 2406 pairs of CID and ETD spectra contained in this data set, 675 fully correct sequences were assigned, which represent a success rate of 28.1%. It is shown that the CompNovo algorithm yields significantly improved sequencing accuracy as compared with published approaches using only CID spectra or combined CID and ETD spectra.

Database independent proteomics analysis of the ostrich and human proteome

“…The occurrence of incomplete sequence information obtainable from either the CID and/or ETD spectra frequently caused this disagreement. It is well documented that CID and ETD can be highly complementary in covering parts of a peptide sequence (14,16,25). Therefore, for every precursor we combined the ETD and CID ion score of the agreeing matches in the top 10 rankings, and took forward the highest-ranking combined score.…”

“…To reduce misassignments, approaches have been suggested based on improved mass accuracy or precision (14,15), combining complementary fragmentation data (14,16,17) or the simplification of fragmentation spectra by using chemical derivatization to manipulate peptide behavior (18). Recently, we introduced a biochemical approach to simplify fragment spectra based on the protease Lys-N (19), which has enzymatic cleavage specificity for the N-terminal side of lysine residues.…”

Peptide Identification by Tandem Mass Spectrometry with Alternate Fragmentation Modes

“…One of the earliest such approaches was the utilization of MS/MS/MS (MS 3 ) acquisition for de novo peptide sequencing (46), later automated with heuristic (47) and optimal (48) algorithms. Similar applications to de novo peptide sequencing were also introduced at about the same time (49) for paired CID and Electron Capture Dissociation (ECD) spectrum acquisition from the same precursors, also later automated for CID/ECD pairs (50) and CID/ETD pairs (51,52). In all cases, automated de novo sequencing was improved by combining ions in the MS 2 /MS 3 or in the paired CID/ExD spectra using either combined peak intensities (47,49,50,52) or statistical scoring models (48,51).…”

Top-down analysis of protein samples by de novo sequencing techniques

“…In the last two decades, several algorithms have been proposed for de novo peptide sequencing from bottomup data, and a few powerful tools appeared, including PEAKS (Ma et al, 2003), PepNovo (Frank and Pevzner, 2005), pNovo (Chi et al, 2010), Lutefisk (Taylor and Johnson, 1997), Sherenga (Dancik et al, 1999), Novor (Ma, 2015), and the program UVnovo (Robotham et al, 2016) recently introduced for the case of 351 nm ultraviolet photodissociation (UVPD) mass spectra. Other achievements comprise methods for complete protein sequencing using multiple enzyme digest and assembly by sequence overlap, possibly referring to a homologous protein sequence (Bandeira et al, 2004(Bandeira et al, , 2007(Bandeira et al, , 2008Liu et al, 2009;Castellana et al, 2010), and a number of alternative approaches benefit from complementarity of mass spectra acquired using different fragmentation techniques from either peptides (Savitski et al, 2005;Datta and Bern, 2008;Bertsch et al, 2009;He and Ma, 2010;Chi et al, 2013;Guthals et al, 2013) or intact proteins (Horn et al, 2000).…”