PEAKS De Novo Sequencing

Peptide de novo sequencing is essential to every well-executed mass spectrometry based protein study. Mass spectrometry labs not using de novo sequencing regularly, limit both fundamental and discovery results.

Features which PEAKS de novo sequencing provide solutions to, include:
• Good quality spectra are often left unexplained after database searching; de novo sequencing is the only recourse.
• Database searches reliably miss unexpected modified peptides, de novo sequence information is a valuable first step in finding these PTM.
• It has been proven that combining de novo sequencing and database protein identification offers optimal results validation.
• False positives are virtually eliminated.
• Sequence tag searching requires good quality de novo sequences to be effective.
• Coverage can be drastically increased by using a sequence tag based search and ms/ms ion search together.
• An incomplete or corrupted database is a common, but an invisible problem in protein identification and characterization research.
• How many peptides/proteins are you missing because of this?
• De novo sequencing as a regular part of your workflow will help catch these.
• When studying species that are not in the public databases, de novo sequencing is the only way to get valuable peptide sequence information.

De novo sequencing is a process where peptide sequences are derived from the masses of their fragments as shown on a tandem mass spectrum. When performing de novo sequencing, no protein sequence database is used for reference.

De novo sequencing is core to PEAKS technology, offering the fastest, most accurate auto de novo sequencing algorithm available. Run auto de novo sequencing on an entire LC run, or a batch of them - process data faster than you can make it (40+ spectra per second). The results are unmatched in accuracy; PEAKS determines at least 3 times as many completely correct sequences as the next best de novo sequencing software. Accurate mass capabilities mean de novo sequencing at 97% accuracy is possible.

With an easy to use, easy to read graphical user interface, PEAKS shows reliable and easy to read confidence scores. Confidence is not only on the peptide sequence, but on each amino acid assignment. PEAKS is the only proteomic mass spectrometry software providing confidence assignment at the amino acid level. Researchers can find the most pertinent information at a glance. Yet, all the information needed for in depth analysis is provided, without cluttering up the display.

PEAKS can find post-translational modifications on peptides when de novo sequencing and position them in the protein sequence.

PEAKS is the only de novo sequencing software specifically tuned to handle data from QTOF, TOF-TOF, Ion Trap, Orbi-Trap and FTMS instruments, while using y and b ions or c and z ions for fragmentation flexibility. It provides a reliable central processing tool for all instrument and experiment types. It is comfortable in any dynamic core facility or demanding private research group.

But PEAKS does not stop at auto de novo sequencing. In addition to automatic de novo sequencing, PEAKS' comprehensive set of assisted manual de novo sequencing tools allow users to edit the results from a PEAKS processed spectrum. Most importantly, PEAKS has an integrated database search for protein identification tool -- a unique approach to protein identification that uses de novo sequencing to help in the search.

Next Page => Learn about hybrid and meta-search protein ID tools.