PMID- 18348511
OWN - NLM
STAT- MEDLINE
DCOM- 20080922
LR  - 20191210
IS  - 1535-3893 (Print)
IS  - 1535-3893 (Linking)
VI  - 7
IP  - 5
DP  - 2008 May
TI  - PepLine: a software pipeline for high-throughput direct mapping of tandem mass 
      spectrometry data on genomic sequences.
PG  - 1873-83
LID - 10.1021/pr070415k [doi]
AB  - PepLine is a fully automated software which maps MS/MS fragmentation spectra of 
      trypsic peptides to genomic DNA sequences. The approach is based on Peptide 
      Sequence Tags (PSTs) obtained from partial interpretation of QTOF MS/MS spectra 
      (first module). PSTs are then mapped on the six-frame translations of genomic 
      sequences (second module) giving hits. Hits are then clustered to detect 
      potential coding regions (third module). Our work aimed at optimizing the 
      algorithms of each component to allow the whole pipeline to proceed in a fully 
      automated manner using raw nucleic acid sequences (i.e., genomes that have not 
      been "reduced" to a database of ORFs or putative exons sequences). The whole 
      pipeline was tested on controlled MS/MS spectra sets from standard proteins and 
      from Arabidopsis thaliana envelope chloroplast samples. Our results demonstrate 
      that PepLine competed with protein database searching softwares and was fast 
      enough to potentially tackle large data sets and/or high size genomes. We also 
      illustrate the potential of this approach for the detection of the intron/exon 
      structure of genes.
FAU - Ferro, Myriam
AU  - Ferro M
AD  - CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Proteomes, Grenoble, 
      F-38054, France.
FAU - Tardif, Marianne
AU  - Tardif M
FAU - Reguer, Erwan
AU  - Reguer E
FAU - Cahuzac, Romain
AU  - Cahuzac R
FAU - Bruley, Christophe
AU  - Bruley C
FAU - Vermat, Thierry
AU  - Vermat T
FAU - Nugues, Estelle
AU  - Nugues E
FAU - Vigouroux, Marielle
AU  - Vigouroux M
FAU - Vandenbrouck, Yves
AU  - Vandenbrouck Y
FAU - Garin, Jerome
AU  - Garin J
FAU - Viari, Alain
AU  - Viari A
LA  - eng
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20080319
PL  - United States
TA  - J Proteome Res
JT  - Journal of proteome research
JID - 101128775
RN  - 0 (Arabidopsis Proteins)
RN  - 0 (Peptides)
SB  - IM
MH  - Algorithms
MH  - Amino Acid Sequence
MH  - Animals
MH  - Arabidopsis/chemistry/cytology/genetics
MH  - Arabidopsis Proteins/*analysis/genetics
MH  - Base Sequence
MH  - Chloroplasts/chemistry/genetics
MH  - *Genome
MH  - *Mass Spectrometry/instrumentation/methods
MH  - Molecular Sequence Data
MH  - Peptides/*analysis/genetics
MH  - Sequence Alignment
MH  - *Software
EDAT- 2008/03/20 09:00
MHDA- 2008/09/23 09:00
CRDT- 2008/03/20 09:00
PHST- 2008/03/20 09:00 [pubmed]
PHST- 2008/09/23 09:00 [medline]
PHST- 2008/03/20 09:00 [entrez]
AID - 10.1021/pr070415k [doi]
PST - ppublish
SO  - J Proteome Res. 2008 May;7(5):1873-83. doi: 10.1021/pr070415k. Epub 2008 Mar 19.