Mass Spectrometer
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Mass Spectrometer

Protein identification with Protein Pilotâ„¢ Software
Protein identification techniques which are essentially peptide identification/correlation techniques, have improved significantly over time. Edman degradation, the preferred technique for many years was simple and very powerful but it was very slow, since it identified one protein at a time. To identify one protein ID in a 60 min gradient would take about seven hours. Compare that to identification done using mass spectrometry routines; it can identify 10 – 50 Proteins in 30 minutes.
Some of the popular mass spectrometry protein identification techniques are peptide mass fingerprinting, sequence tag identification and ms/ms peptide identification. In ms/ms peptide identification a peptide is broken up using a mass spectrometer and the fragment ion masses are then used to search a sequence database.
There is intense competition among companies that operate in the mass spectrometry space to be the best at protein identification but with a vastly simplified user interface and the power to search for hundreds of modifications simultaneously, the Protein Pilot™ Software, developed by Absciex sets a new standard for quality and quantity of results in protein identification and biomarker discovery. The system is powerful, easy to use and provides tools to help you search, identify, and analyze hundreds of proteins and quickly find the information you need. Key features of Protein Pilot™ Software are:-
1. Tag-based probabilistic approach:
Search for hundreds of modifications and variants without an explosion of false positives using the innovative Paragon™ algorithm.
2. Robust protein reporting:
Determine and report the number of proteins and isoforms actually detected, including ambiguity among multiple accessions with the industry leading Pro Group™ Algorithm.
3. Integrated, rigorous false discovery rate (FDR) analysis:
Analyze the specificity and quality of your results at the highest level with decoy database searching.
Targeted, hypothesis driven protein/peptide quantitation using MRM (Multiple Reaction Monitoring) enables you to detect and measure hundreds of proteins in a given experiment at high sensitivity.
Protein Pilot™ Software has changed the protein identification and peptide quantitation paradigm. One doesn't have to specify details like mass tolerances, individual modifications, expected fragment ion types, or exceptions to cleavage rules. Simply enter the sample information you know, and the algorithm automatically optimizes the settings.
The Protein Pilot™ Software user interface is very easy to view and navigate through protein identification and quantitation results. The Protein ID view displays the proteins detected and the protein-peptide associations for each protein group, including the raw MS/MS spectrum and matching peaks. The Protein Quant view displays each measured protein ratio color-coded by P-value, so one can quickly see changes in expression levels.
Protein Pilot™ Software includes an automatic false discovery rate (FDR) analysis that gives you a rigorous defense of the quality of your results, using both conventional FDR analysis as well as novel extensions. If your typical workflow is gel-based analysis, you can submit PMF and PMF-combined searches on TOF/TOF data to Mascot for identification of gel spots.
It has ultimate flexibility and control as you can search data from any instrument. Protein Pilot™ FDR analysis supports instruments from several manufacturers. An open parameter control function allows you to add support for instruments not already included. A translation file is also available for accessing parameters such as new modifications, instrument settings, and digests agents.
Additional details & trial software downloads are available at www.absciex.com.
About the Author
Ryan Harris is a prolific writer for issues pertaining to the life science industry and has authored many research papers specifically on proteomics. His in-depth knowledge pertaining to mass spectrometry solutions is respected across the industry.
How does a mass spectrometer work? ?
I know a mass spectrometer is the most accurate way to determine the mass of an element...But how does it work?
How a mass spectrometer works
The basic principle
If something is moving and you subject it to a sideways force, instead of moving in a straight line, it will move in a curve - deflected out of its original path by the sideways force.
Suppose you had a cannonball travelling past you and you wanted to deflect it as it went by you. All you've got is a jet of water from a hose-pipe that you can squirt at it. Frankly, its not going to make a lot of difference! Because the cannonball is so heavy, it will hardly be deflected at all from its original course.
But suppose instead, you tried to deflect a table tennis ball travelling at the same speed as the cannonball using the same jet of water. Because this ball is so light, you will get a huge deflection.
The amount of deflection you will get for a given sideways force depends on the mass of the ball. If you knew the speed of the ball and the size of the force, you could calculate the mass of the ball if you knew what sort of curved path it was deflected through. The less the deflection, the heavier the ball.
Next time, you google your question.
The Mass Spectrometer




































































































