protein bioinformatics and systems biology nathan edwards department of biochemistry and molecular...
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Protein bioinformatics and systems biology
Nathan EdwardsDepartment of Biochemistry and
Molecular & Cellular Biology
Georgetown University Medical Center
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Unannotated Splice Isoform
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Unannotated Splice Isoform
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Halobacterium sp. NRC-1ORF: GdhA1
K-score E-value vs PepArML @ 10% FDR Many peptides inconsistent with annotated
translation start site of NP_279651
0 40 80 120 160 200 240 280 320 360 400 440
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PepArML Meta-Search EngineNSF TeraGrid1000+ CPUs
Edwards LabScheduler &80+ CPUs
Securecommunication
Heterogeneouscompute resources
Single, simplesearch request
Scales easily to 250+ simultaneous
searches
X!Tandem,KScore,OMSSA,
MyriMatch,Mascot(1 core).
X!Tandem,KScore,OMSSA,
MyriMatch.
Amazon AWS
False-Discovery-Rate Curves
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PeptideMapper Web Service
I’m Feeling Lucky
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PeptideMapper Web Service
I’m Feeling Lucky
If a tree falls in the forest…
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Nascent polypeptide-associated complex subunit alpha
Long form is "muscle-specific" Exon 3 is missing from short form
Peptide identifications provide evidence for long form only 9 peptides are specific to long form 6 peptides are found in both isoforms
Urn with balls of 15 different colors p-value of observed spectral counts: 7.3E-8
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E:\Yersinia Work\yr_inclusion 3/11/2009 3:43:13 PM yrohdei
RT: 19.04 - 25.39
19.5 20.0 20.5 21.0 21.5 22.0 22.5 23.0 23.5 24.0 24.5 25.0
Time (min)
0
20
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100
0
20
40
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Re
lative
Ab
un
da
nce
25.3619.9919.93
25.2720.04 25.2319.89 23.0322.97 23.08
20.1019.83 23.64 25.1923.7022.88 24.6324.5720.1422.82
20.2019.7822.7220.2519.48
22.5220.41 22.0821.8420.60 21.04
20.00
21.03 21.46
NL: 1.66E8
TIC MS yr_inclusion
NL: 1.01E7
TIC F: FTMS + p ESI d Full ms2 [email protected] [195.00-2000.00] MS yr_inclusion
yr_inclusion #1937-2437 RT: 19.45-24.36 AV: 21 NL: 4.80E4F: FTMS + p ESI d Full ms2 [email protected] [195.00-2000.00]
200 400 600 800 1000 1200 1400 1600 1800 2000
m/z
0
10
20
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Re
lative
Ab
un
da
nce
576.83z=2
840.16z=7
720.39z=2 903.81
z=3785.41
z=4694.62
z=4
584.57z=4
928.49z=4559.55
z=41804.48
z=?992.53
z=3200.78z=?
329.71z=?
1253.14z=?
555.29z=4
1610.27z=?
1883.75z=?
1491.23z=?
1118.93z=?
1666.89z=?
1345.30z=?
461.16z=?
756.70 +8 MW 6044.11
Top-down CID Protein Fragmentation from Y. rohdei
Match to Y. pestis 50SRibosomal Protein L32
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Phyloproteomics of Y. rohdei
Protein Sequence 16S-rRNA Sequence
Example Glycopeptide CID Fragmentation Spectrum
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Hap
tog
lob
in (
HP
T_H
UM
AN
)
NLFLNHSE*NATAK
MVSHHNLTTGATLINE
VVLHPNYSQVDIGLIK
Haptoglobin standard
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• N-glycosylation motif (NX/ST)
* Site of GluC cleavagePompach et al. Journal of Proteome Research 11.3 (2012): 1728–1740.