Wednesday, March 27, 2013

PEAKS de novo sequencing on 3.4 million MS2 spectrum

It is unbelievable how fast the mass spectrometry data can grow in size. A decade ago, when Dr. Bin Ma created PEAKS, a data file containing hundreds of spectrum is already considered large. Now we are seeing dataset over a million spectrum on a regular basis. On this scale, it is quite challenging for proteomics software to analyze the data within a reasonable amount of time under finite computing resources.

I recently received a large dataset from one of our collaborators. The data contains 3.4 million MS2 spectrum in total (about 160 hours LC for all the samples) and it is generated on a Thermo Orbitrap instrument.

I now have the project created and started de novo sequencing on all the spectrum in one go. It will take a while until the job completion.

Stay tuned!


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    1. PEAKS uses a comprehensive scoring system to provide accurate de novo peptide sequencing results. Unique to PEAKS is the Local Confidence Score Assignment Writing Service the likelihood of each amino acid assignment in a resultant peptide. The local confidence score extends the accuracy to the amino acid level.

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