A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications.

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Abstract Text:

Bingwen Lu,Ting Chen,

MOTIVATION: Tandem mass spectrometry combined with sequence database searching is one of the most powerful tools for protein identification. As thousands of spectra are generated by a mass spectrometer in one hour, the speed of database searching is critical, especially when searching against a large sequence database, or when the peptide is generated by some unknown or non-specific enzyme, even or when the target peptides have post-translational modifications (PTM). In practice, about 70-90% of the spectra have no match in the database. Many believe that a significant portion of them are due to peptides of non-specific digestions by unknown enzymes or amino acid modifications. In another case, scientists may choose to use some non-specific enzymes such as pepsin or thermolysin for proteolysis in proteomic study, in that not all proteins are amenable to be digested by some site-specific enzymes, and furthermore many digested peptides may not fall within the rang of molecular weight suitable for mass spectrometry analysis. Interpreting mass spectra of these kinds will cost a lot of computational time of database search engines. OVERVIEW: The present study was designed to speed up the database searching process for both cases. More specifically speaking, we employed an approach combining suffix tree data structure and spectrum graph. The suffix tree is used to preprocess the protein sequence database, while the spectrum graph is used to preprocess the tandem mass spectrum. We then search the suffix tree against the spectrum graph for candidate peptides. We design an efficient algorithm to compute a matching threshold with some statistical significance level, e.g. p = 0.01, for each spectrum, and use it to select candidate peptides. Then we rank these peptides using a SEQUEST-like scoring function. The algorithms were implemented and tested on experimental data. For post-translational modifications, we allow arbitrary number of any modification to a protein. AVAILABILITY: The executable program and other supplementary materials are available online at: http://hto-c.usc.edu:8000/msms/suffix/.

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Publishing Authors By Initials

B Lu,T Chen,

For similar biochemical phenomena, metabolism, and nutrition: biochemical phenomena: structure-activity relationship research abstracts see: biochemical phenomena, metabolism, and nutrition: biochemical phenomena: structure-activity relationship research

PUBMED ID PMID:

MEDLINE DATE:

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Bioinformatics (Oxford, England)

VOLUME: 19 Suppl 2

Page Numbers: ii113-21

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 3

MONTH: Oct

YEAR: 2003

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9808944

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Keywords Mesh Terms:

KEYWORDS: Structure-Activity Relationship

MESH TERMS: methods

Chemical & Substance for Abstract: A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications.

AFFILIATION: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Country: England

AGENCY: United States NCRR

GRANT: 1-R01-RR16522-01

ACRONYM: RR

MEDLINETA: Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications Related Publications

• A new function of BMP4: dual role for BMP4 in regulation of Sonic hedgehog expression in the mouse tooth germ.
• An experimental study of anti-angiogenesis with recombinant human kringle 5.
• Application of Nd-Yag laser for gingivoplasty during orthodontic treatment.
• Clinical study of alveolar vertical distraction osteogenesis for implant.
• Enzyme-linked immunosorbent assay for the determination of p21-activated kinase activity.
• Hemorheology and expression of neutrophil adhesion molecules CD18 and CD62L in pancreatic microcirculation of Caerulein induced experimental acute pancreatitis.
• Lack of effect of dietary alpha-tocopherol on chemically induced hepatocarcinogenesis in rats.
• Prostaglandin E2 is involved in the increase of cytochrome P-450 2B1 expression by alpha-tocopheryl succinate in primary rat hepatocytes in the presence of phenobarbital.
• Rescue of cleft palate in Msx1-deficient mice by transgenic Bmp4 reveals a network of BMP and Shh signaling in the regulation of mammalian palatogenesis.
• Transgenically ectopic expression of Bmp4 to the Msx1 mutant dental mesenchyme restores downstream gene expression but represses Shh and Bmp2 in the enamel knot of wild type tooth germ.
• [A study on apoptosis and activity of SAPK/JNK in adrenocortical cells induced by cadmium chloride]
• [A study on central zone contour of tooth-crown vesticular surface among young people with normal occlusion]
• [Bone-inducing activity of human bone morphogenetic protein-2 102 peptide]
• [Comparative effects of tensiomin and sodium dimercaptosulphonate on the serum sulfydryl and anticopper of the patients with Wilson's disease]
• [Effects of fluoride on the expression of c-fos and c-jun genes and cell proliferation of rat osteoblasts]
• [Establishment of EBV-immortalized lymphoblast cell lines from three Chinese Fanconi anemia patient and their subtyping]
• [Experimental methods for mechanically stimulating the cells in vitro]
• [Focal adhesion kinase]
• [GATA-2 gene expression in leukemia patients and its significance]
• [Genetic polymorphisms of cytochrome P450 1A1 and susceptibility of early-onset Parkinson's disease]
• [Influence of chemotherapy on hematopoietic microenvironment and effect of autologous bone marrow stromal cell infusion on the recovery of hematopoiesis after chemotherapy]
• [Influence of the stratum corneum and dermis of the skin on the percutaneous absorption of fluorouracil delivered through skin patch]
• [Isolation, cultivation and identification of neural stem cell from human embryonic CNS]
• [Melanoma antigen-3 expression in human hepatocellular carcinoma]
• [Novel full-length cDNA cloning from normal adrenal gland and pheochromocytoma and functional prediction]
• [Preparation and application of a new chloromethylstyrene encapsulated silica single anion column]
• [Study on the intestinal microbial colonization resistance in patients with chronic severe hepatitis]
• [Synergetic transactivating functions of HCV core and truncated HBV middle surface protein]
• [Telomerase activity and cellular apoptosis of bladder cancers]
• [The apolipoprotein E gene polymorphism in children with steroid-resistant idiopathic nephrotic syndrome]