Shotgun Protein Sequencing statistics

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Shotgun Protein Sequencing specifications


Unique identifier OMICS_21810
Name Shotgun Protein Sequencing
Alternative name MS/MS spectra assembly
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained Yes


  • person_outline Nuno Bandeira <>

Additional information

Publications for Shotgun Protein Sequencing

Shotgun Protein Sequencing in publications

PMCID: 5408190
PMID: 28346332
DOI: 10.3390/toxins9040116

[…] 500ms full scan time-of-flight mass spectrometry (tof-ms) data over the mass range 350–2000. the data was acquired and processed using analyst tf 1.6 software (sciex, concord, on, canada)., for shotgun protein sequencing, whole crude venom from a representative individual of each group was reduced, alkylated, digested and submitted for lc-ms/ms analysis. this was performed by first […]

PMCID: 4999880
PMID: 27562653
DOI: 10.1038/srep31730

[…] for the data analysis, including de novo sequencing directly from tandem mass spectra and database search methods that use existing protein sequence databases. more specifically, various versions of shotgun protein sequencing (sps) used cid/hcd/etd fragmentation methods and other techniques to increase the coverage, and have achieved significant progress in attempt to fully sequence proteins, […]

PMCID: 2746175
PMID: 19735572
DOI: 10.1186/1743-8454-6-10

[…] with long-standing shunts for congenital hydrocephalus. cell-free csf was subjected to ultracentrifugation to yield supernatants and pellets that were examined by transmission electron microscopy, shotgun protein sequencing, electrophoresis, western blotting, lipid analysis, enzymatic activity assay, and immuno-electron microscopy., over 3,600 csf proteins were identified from repeated shotgun […]

PMCID: 2704378
PMID: 19609354
DOI: 10.1371/journal.pgen.1000565

[…] rule out other recoding events based solely on sequence comparisons. to eliminate the possibility of other such changes in the genetic code, and to experimentally verify the uga stop→trp recoding, shotgun protein sequencing by mass spectrometry was used to sequence peptides derived from cicada bacteriomes. these peptide sequences ruled out any other codon reassignments, and experimentally […]

PMCID: 2718660
PMID: 18785330
DOI: 10.1093/bioinformatics/btn184

[…] may be attenuated by generating overlapping peptides and combining the resulting ms2 spectra to yield higher accuracy de novo sequences—examples include 16o/18o labeling (shevchenko et al., ) or shotgun protein sequencing (bandeira et al., , ). while shotgun protein sequencing was shown to work well for low-complexity samples it remains unclear how it will scale up for complex samples. […]

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Shotgun Protein Sequencing institution(s)
From the Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
Shotgun Protein Sequencing funding source(s)
Supported by NIGMS, National Institutes of Health Grant 1-R01-RR16522.

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