Transcript SORCERER-Platform-Overview - Sage

“SORCERER Platform Overview”
Sorcerer product line
• Sorcerer 2 — well-established standard
– Self-contained tower (or 2U rack unit)
– Can fit under bench, shared by lab
– One high-end processing node, with integrated
storage
– Good match for single Orbi or similar
• Sorcerer Enterprise — new HT platform
– Pre-integrated rack cabinet
– Goes in server room, shared site-wide
– Includes multinode blade server with
high capacity storage subsystem
– Ideal for multi-instrument throughput
Sorcerer’s Primergy hardware platform
• Sorcerer 2 on Primergy platform
– Came out in 2008
– Introducing 3rd rev in Q3 this year
– Further uptick in CPU and system
components
• SNR-Fujitsu partnership
developed with Sorcerer 2
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Joint platform design
Testing and tuning
Manufacturing
Worldwide field support
• Enables Enterprise platform
– Collaboration for optimal blade
server, storage and interconnect
design
– Result: takes throughput to next level
with high performance and scalability
Sorcerer 2 server evolution
System Model
‘Silver box” (rev2)
Primergy TX300S4
Primergy TX300 S5
Primergy TX300 S6
# CPUs
2
2
2
2
Cores/CPU
Dual
Quad
Quad
Quad
# Sorcerer jobs
6
8
8
8
CPU architecture
Paxville
Harpertown
Nehalem
Westmere
Rel CPU integer
throughput.*
44% (est.)
100%
204%
215%
2007
* SPECint*_rate_base2006
2008
2009
2010
2011
Sorcerer Enterprise platform
• Goal: scalable analysis throughput for multiple instruments
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More data to analyze, more data to keep
Faster scan rates, e.g. Orbi Velos
Multi-vendor instrumentation
Broad array of applications and downstream analysis
Needs most sensitive searching
• Solution: Sorcerer Enterprise on blade server
– Primergy BX900 server with up to 18 blades
• Each blade has more processing power than a Sorcerer 2
– Eternus DX80
• ~9TB disk space in base configuration, expandable up to ~180TB
• (Sorcerer 2: ~2TB available disk space)
• RAID-6 for extra data integrity and redundancy
Sorcerer Enterprise “under the hood”
• Components in base config
– Primergy BX9oo blade server:
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10U (17½”) chassis with 18 slots
1 build-in high speed interconnect blade
2× (up to 18×) BX920 blades, each with:
8 ‘Nehalem’ cores, 36GB RAM,
2×76GB fast SAS drives, built-in ethernet
– Eternus DX80 disk storage system
• Each module can hold 12 disks
(450GB SAS or 1TB nearline)
• iSCSI fast connection
– Integrated in rack with UPS,
network switch etc.
• Externally
– One Ethernet port, one IP address
(“plug-and-play”)
Sequest 3G
• What is it?
– Next generation Sequest
– keeps (and extends) its gold standard sensitivity
– evolves for modern proteomics
• Key benefits of the technology
– optimized for high-throughput searching of large data sets
– digital signal processing techniques improve sensitivity for noisy
spectra
– provides robust PTM search
– support for new fragmentation techniques such as ETD
– extensions to SEQUEST 3G enable multiple similarity scores for
improved specificity
Sequest 3G
on Sorcerer
Key Steps:
1. Fast but accurate spectrum
matching that uses ppm
mass accuracy
2. Complete "on the fly"
consideration of chosen
PTMs
3. All candidate matches (not
just a "short list") get
rigorous cross-correlation
scores ...
4. ... to enable most sensitive
ranking and effective
compilation of results
5. Comprehensive XCorrs
also allow reliable E-value
results for simple
interpretation, as well as
computation of legacy
SEQUEST scores
Sorcerer PE Software V4.0 beta
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Sorcerer Enterprise distributed searching
TPP v4.3.1
Support for Scaffold V3.0
Sequest 3G initial release
Muse: new scripts
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Integration with DTASelect, Census, APEX, etc.
New “Versasearch” combined ETD/CID analysis
• New license manager facilitates better performance with more
system resources
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Better Sorcerer Enterprise performance
• Coming Msconvert support will handle Xcalibur 2.1 Raw files
• Bug fixes and minor updates
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Muse Example: DTASelect and
Census
Great tools for filtering, reporting and quant from Yates Lab
– Available from Yates lab (fields.scripps.edu)
– We recommend it for SILAC etc. (commercial offering in development)
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On Sorcerer, install scripts and run census_select.muse
– Runs DTASelect, then Census
– View DTASelect report directly from Sorcerer Web GUI
– Runs Census pre-analysis using search results and supplied params/config
census_select.muse -c ~/custom/census/census_config_silac.xml
VersaSearch™ for combined
CID/ETD
• Unified search accommodates ETD variations
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All-CID, all-ETD, alternating, & decision tree
• Peptide terminus mods to account for b vs c, y vs. z-radical
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Post-processing to define “true” vs. “decoy”
• Post-search re-scoring provides other similarity scores
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RAW
E.g. binomial scores
User-defined fragmentation models
Extract
peaklist
peaks SEQUEST 3G
Peptide ID
w/ terminus mods
Determine
CID vs. ETD
Tag
True/Decoy
w/ MUSE
pep
hits
Peptide FDR
Protein prot hits
Inference