Protein identification using top-down.
In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set.
Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, San Diego, California 92093, USA.
Xiaowen
X
Liu
Yakov
Y
Sirotkin
Yufeng
Y
Shen
Gordon
G
Anderson
Yihsuan S
YS
Tsai
Ying S
YS
Ting
David R
DR
Goodlett
Richard D
RD
Smith
Vineet
V
Bafna
Pavel A
PA
Pevzner
D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D003627:Data Interpretation, Statistical; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D008970:Molecular Weight; D010449:Peptide Mapping / Q000379:methods*; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D012441:Saccharomyces cerevisiae; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism; D012486:Salmonella typhimurium; D012984:Software; D053719:Tandem Mass Spectrometry
D001426:Bacterial Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins