Article

Efficiency improvement of peptide identification for an organism without complete genome sequence, using expressed sequence tag database and tandem mass spectral data.

Korea Basic Science Institute, 52 Yeo-Eun Dong, Yusung-gu, Daejeon 305-333, Korea.
PROTEOMICS (impact factor: 4.51). 01/2004; 3(12):2305-9. DOI:10.1002/pmic.200300620 pp.2305-9
Source: PubMed

ABSTRACT We compared peptide identification by database (DB) search methods with de novo sequencing results for proteomics study in an organism without genome sequence information. When the former was done by searching the Expressed Sequence Tag (EST) DB of the sample organism or the NCBI nonredundant (nr) protein DB of green plants using either the MASCOT or SEQUEST software program, it was confirmed that the former is as accurate as the latter. Peptides identified from EST DB were twice as many as those from the nr protein DB, in spite of the fact that the EST DB has less data (26 222 EST) than the NCBI nr protein DB (224 238). This study demonstrates that EST DB with tandem mass spectra can be used reliably for high-throughput proteomics studies in an organism without genome information.

0 0
 · 
0 Bookmarks
 · 
22 Views
  • Source
    Article: Cardiac-specific overexpression of catalase prolongs lifespan and attenuates ageing-induced cardiomyocyte contractile dysfunction and protein damage.
    Shan Wu, Qun Li, Min Du, Shi-Yan Li, Jun Ren
    [show abstract] [hide abstract]
    ABSTRACT: 1. Oxidative stress plays a role in senescence-associated organ deterioration. This is supported by the beneficial effects of anti-oxidants against ageing-related organ damage, although their role in cardiac ageing has not been elucidated. 2. The aim of the present study was to examine the impact of cardiac-specific overexpression of catalase, an enzyme for H(2)O(2) detoxification, on cardiac contractile function and protein damage in young (3-4 months) and old (26-28 months) male mice. Lifespan was analysed using the Kaplan-Meier survival curve. Cardiomyocyte contractile indices at various stimulus frequencies (0.1-5.0 Hz) were analysed, including peak shortening (PS), time to 90% PS, time to 90% relengthening (TR(90)) and maximal velocity of shortening/relengthening (+/-dL/dt). Protein damage was assessed using protein carbonyl formation. Catalase transgenic mice showed longer lifespan than wild-type FVB mice. The catalase transgene itself did not alter bodyweight or organ weight, or myocyte function. Ageing depressed +/-dL/dt and prolonged TR(90), but had no effect on other indices in FVB mice. Increased frequency triggered decreases in PS amplitude were exaggerated in aged FVB myocytes. Interestingly, ageing-induced mechanical defects were significantly attenuated in myocytes from catalase mice. Protein carbonyl formation was elevated in aged FVB compared with young FVB mice, which was significantly diminished in catalase mice. The proteomes of the myocardium of young or old FVB and catalase mice were compared using two-dimensional gel electrophoresis and mass spectrometry. Six proteins with differential expression between young and old FVB groups were tentatively identified, some of which were reversed by catalase. 3. In summary, the present data suggest that catalase protects cardiomyocytes from ageing-induced contractile defects and protein damage.
    Clinical and Experimental Pharmacology and Physiology 34(1-2):81-7. · 1.85 Impact Factor
Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. The impact factor represents a rough estimation of the journal's impact factor and does not reflect the actual current impact factor. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.

Keywords

de novo sequencing results
 
Expressed Sequence Tag
 
former
 
genome information
 
genome sequence information
 
green plants
 
high-throughput proteomics studies
 
NCBI nonredundant
 
NCBI nr protein DB
 
nr
 
nr protein DB
 
peptide identification
 
Peptides
 
proteomics study
 
sample organism
 
SEQUEST software program
 
tandem mass spectra
 

Kyung-Hoon Kwon