Although a variety of algorithms have been demonstrated to provide accurate matches between tandem mass spectra and sequences, all suffer from an inability to provide matches to poor quality spectra. Most algorithms are very accurate for peptides that follow general rules of fragmentation, but a subset of amino acid sequences and more highly charged peptide ions deviate from these rules. What can we do to improve the system. Does anyone know algorithms designed with high selectivity and sensitivity?

Hi,
I must claim an inability to understand what it is you are asking about. Can you help me by defining and if possible giving examples of a few terms "tandem mass spectra" and "poor quality spectra". Also with your indulgence can you explain what the general rules of fragmentation for peptides are or where I can read about this? FInally can you point me to the available algorithms you mention?
Thanks very much,
As quoted in Tomb Raider "I am amused by my own ignorance"

Scot E. DOwd Ph.D. said:

Hi, I must claim an inability to understand what it is you are asking about. Can you help me by defining and if possible giving examples of a few terms "tandem mass spectra" and "poor quality spectra". Also with your indulgence can you explain what the general rules of fragmentation for peptides are or where I can read about this? FInally can you point me to the available algorithms you mention? Thanks very much, As quoted in Tomb Raider "I am amused by my own ignorance"

Large-scale proteomics experiments can present big challenges for data analysis. Most database searching algorithms can identify amino acid sequences from tandem mass spectra ( you will find details about tandem mass spectrometry in chemistry books) showing good fragmentation and signal-to-noise ratio. Spectra of poor- quality are those containing aberrant fragmentations. In tandem mass spectrometry(MS/MS), gas phase peptide ions undergo collision-induced dissociation with molecules of an inert gas such as helium or argon. This is one method of fragmentation or dissociation. Other methods of dissociation have been developed, such as electron capture dissociation , surface induced dissociation this goes on and on and on....

According to Webster's New World Medical Dictionary:

Tandem mass spectrometry: An instrument used in medical laboratories consisting of two mass spectrometers in series connected by a chamber known as a collision cell. The sample to be examined is essentially sorted and weighed in the first mass spectrometer, then broken into pieces in the collision cell, and a piece or pieces sorted and weighed in the second mass spectrometer. Tandem mass spectrometry is used in newborn screening to detect molecules such as amino acids (the building blocks of proteins) and fatty acids.

Generally, I believe Sandy is saying that the algorithms work fine for well-defined, well-behaved amino acids, however, there are some that are the exception (i.e. don't fragment well in the collision cell) and therefore are hard to identify (specify?) by the second mass spectrometer, because of their inherent "poor quality spectra". Is that close?

Neil Custer said:

According to Webster's New World Medical Dictionary: Tandem mass spectrometry: An instrument used in medical laboratories consisting of two mass spectrometers in series connected by a chamber known as a collision cell. The sample to be examined is essentially sorted and weighed in the first mass spectrometer, then broken into pieces in the collision cell, and a piece or pieces sorted and weighed in the second mass spectrometer. Tandem mass spectrometry is used in newborn screening to detect molecules such as amino acids (the building blocks of proteins) and fatty acids. Generally, I believe Sandy is saying that the algorithms work fine for well-defined, well-behaved amino acids, however, there are some that are the exception (i.e. don't fragment well in the collision cell) and therefore are hard to identify (specify?) by the second mass spectrometer, because of their inherent "poor quality spectra". Is that close?

Thank you Neil you explained well.