News & Updates

  • Oct 4 John Yates seminar

    at 3:30 pm in Foege Auditorium on 10/9.
  • Oct 2 Bioinformatics Positions

    available in the Kelleher at Northwestern.
  • Oct 1 Fall PacMass

    is in 2 days at UW SLU. 5:30 pm social hour, 6:30 pm speaker.
  • Sep 10 US HUPO Contest

    US HUPO 2020 is in Seattle! Submit your design for the conference t-shirts here.
  • Sep 6 Comet 2019.01 rev. 1

    is now installed on our systems. Click here to see the release notes.
  • Aug 19 Comet 2019.01 rev. 0

    is now installed on our systems. Click here to see the release notes.
  • June 19 Cascadia Proteomics Symposium

    will be held July 8-9 with Alexey Nesvizhskii as Keynote speaker. Information at here.
  • March 14 PacMass Spring Meeting

    Held here at SLU on Tues 3/26 at 7:30.
  • Dec 10 Comet 2018.01 rev. 3

    is now installed on our systems. Click here to see the release notes.
  • Nov 13 PacMass at Hutch

    Tomorrow Wednesday Nov. 14 at Fred Hutch. Members Night Social and Poster Session.
  • Oct 11 Thermo Software Update

    Thermo has a critical software update aimed at anyone who has installed Xcalibur/Foundation software on their computers, even if the software has been deleted. A tad ominous.
  • Sep 28 PacMass at SLU

    Wednesday Oct. 24, UW SLU Bldg C. 5:30 social hour, 6:30 presentation. Prof. Daniel Promislow is speaking.
  • Jun 13 Comet 2018.01 rev. 2

    is now installed on our systems. Click here to see the release notes.
  • Jun 12 PacMass meeting tomorrow!

    Dan Raftery will be speaking at 6:30PM (social hour begins 5:30PM) here at UW SLU Building C, room 123AB.
  • Jun 11 Ben Garcia talk at SLU

    His talk at noon in the UW SLU Brotman Auditorium on June 18 is titled "Quantitative Proteomics for Understanding Modified Proteins and Proteomes".
  • May 17 Comet 2018.01 rev. 1

    is now installed on our systems. Click here to see the release notes.
  • Apr 26 Comet 2018.01 rev. 0

    is now installed on our systems. Click here to see the release notes. If you're a local UWPR user, sign up here to join the UWPR computational mailing list.
  • Apr 27 66th ASMS Conference

    is June 3-7, 2018 in San Diego. Advanced registration closes on Monday 4/30.
  • Feb 20 Comet 2017.01 rev. 4

    is now installed on our systems. Very minor maintenance release with change related to deltaCn values of lower (not top ranked) hits.
  • Feb 14 1st Annual North America MS

    Summer School with an amazing list of instructors. Apply now; no cost to participate and travel awards available.
  • Jan 26 Postdoc position available

    At the ICCVS (cancer vaccine science) in Gdansk.
  • Jan 26 PacMass Winter Meeting 2018

    PacMass will feature Prof. Mike Gelb here at UW SLU on Feb 13th.
  • Jan 5 Comet Update

    Comet has been updated to version 2017.01 rev. 3 on our UWPR systems.
  • Oct 19 PacMass

    Member's Night Social and Poster Session at the Fred Hutch on 11/1.
  • Sep 25 Fall PacMass

    here at UW SLU this Wednesday 9/27; social hour starts at 5:30PM.
  • Jul 12 Job at Vividion Therapeutics

    Vividion is a biotech startup in San Diego (founded by Ben Cravatt at TSRI) and they're looking for a Proteomics Scientist. Could be you!
  • Jul 6 Job at Biognosys

    Biognosys is looking to expand their US presence and is looking for Scientific Business Developers which are people who can "talk proteomics".
  • Jun 27 Mascot server

    Mascot has been updated to 2.6.1. We started from scratch so send me (Jimmy) a note if you had access before and need your account re-created.
  • May 17 UWPR computation mailing list

    All UWPR specific computational announcements are going to be made through the UWPR_computation mailing list. Sign up if you're interested.
  • May 8 PacMass Spring meeting

    will feature Brendan MacLean speaking about Skyline on Wed May 17 here at UW SLU.
  • May 2 Comet 2016.01 rev. 3

    is now live on UWPR systems.
  • Apr 24 Postdoc at UNC

    Dough Phanstiel is a former colleague of mine; he's now at UNC and looking for a postdoc with some computational background. If you're interested in moving to Chapel Hill or possibly getting involved with genomic work studying chromatin structure, contact Doug for more info.
  • Feb 21 TPP updated to 5.0

    I just updated our version of TPP to the latest 5.0. For users with access to running this tools, this does require a setup step. See this page for info.
  • Feb 1 PacMass meeting

    Prof. Heather Bean from ASU will give a talk on proteomics and biomarkers of lung infection on March 1st here at UW SLU, 6:30PM at the Orin Smith Auditorium.
  • Jan 26 Nuno Bandeira seminar

    February 1st at 3:30PM in the Foege Auditorium titled "Revealing deep diversity in the human proteome with mass spectrometry big data".
  • Apr 27 Multiple positions open

    in both the Jim Bruce lab at UW and the Danielle Swaney lab at UCSF. Check out the job postings if you're in the market.
  • Sep 27 Autumn PacMass

    Autum 2016 PacMass is scheduled for Oct. 5 at UW SLU. Come hear a talk from Dr. Yi He of UW Medicine on lipoprotein structure, crosslinking and mass spectrometry.
  • Aug 25 Proteomics Blog

    News has been slow so here's a link to Ben Orsburn's proteomics blog for those of you who might not be aware of it.
  • Jun 28 Cascadia conference

    being held July 11-12 at ISB just a few blocks from us.
  • Apr 27 Data access issues

    Anyone experience login issues to view your search results, please see the explanation and suggested solutions on this page
  • Apr 6 Comet 2016.01 rev. 2

    is now live on UWPR systems.
  • Mar 29 Comet 2016.01 rev. 1

    is now live on UWPR systems.
  • Mar 16 Comet 2016.01 rev. 0

    is now live on UWPR systems.
  • Feb 24 Lunch Seminar

    Martin Sadilek will be giving 2 lunch seminars on heat stabilization as a sample preservation technique. 3/8 at noon in Chemistry CHB102 and 3/9 at noon at SLU room E130A. Lunch sandwiches provided!
  • Feb 24 PacMass

    tonight at 5:30 here at UW SLU. Dr. Daniela Grabs speaking.
  • Jan 22 Comet 2015.02 rev. 5

    is now live on UWPR systems. Minor maintenance release.
  • Jan 19 Comet 2015.02 rev. 4

    is now live on UWPR systems. Minor maintenance release.
  • Dec 14 TPP course at ISB

    The next TPP course will be held at ISB in Seattle from 2/1 to 2/5/2016. Go register now if you're interested in learning more about the tools.
  • Nov 24 Comet 2015.02 rev. 3

    is now live on UWPR systems. Small maintenance release to address mgf parsing, n-term mods, etc.
  • Oct 28 PacMass

    Member's night Social and Poster Session on 11/4/2015 at the Fred Hutch.
  • Oct 16 Life Science Research Weekend

    Come visit the mass spec booth at the Life Science Research Weekend held at the Pacific Science Center. The mass spec booth will be there on 11/6 and 11/8.
  • Oct 10 Comet 2015.02 rev. 2

    is now live on UWPR systems. Small maintenance release to fix binary mods.
  • Oct 10 Comet 2015.02 rev. 1

    has been released and is now live on UWPR systems.
  • Sep 28 PacMass tomorrow

    here at UW SLU. Social hour starts at 5:30.
  • Sep 10 Nature Milestones

    A nice series of articles highlighting some of the most influential developments in the history of mass spectrometry.
  • Jul 31 Comet 2015.02 rev. 0

    has been released. See the release notes. This version has not been released on the UWPR systems yet new functionality benefits very few users.
  • Jul 31 World HUPO

    will be in Vancouver, BC, Canada on 9/27-9/30. If you're attending, take the 2.5 hour drive south to visit us here at the UWPR.
  • Apr 28 Comet 2015.01 rev. 2

    is now live on UWPR systems. See the release notes for info on changes.
  • Apr 22 Peach lunch delivery

    sign up for it here for SLU.
  • Mar 6 Comet 2015.01 rev. 1

    is now live on UWPR systems. See the release notes for info on changes.
  • Mar 2 Comet 2015.01 rev. 0

    is now live on UWPR systems. See the release notes for info on changes.
  • Mar 2 Congratulations

    to Eva Jahan for being accepted into the UW Medical school!
  • Feb 11 MSBM Summer School

    in Dubrovnik is July 5-11. Registration is open now.
  • Feb 9 Mike Senko from Thermo

    is speaking at the UW Foege Auditorium this Wed. Feb 11 at 3:30PM.
  • Feb 4 PacMass meeting

    is tomorrow (Thurs) here at UW SLU. Dick Smith from PNNL is the speaker.
  • Nov 24 TPP updated to 4.8.0

    on the UWPR systems.
  • Nov 19 MassSpecUtils update

    The latest version is now available at the MassSpecUtils website.
  • Nov 18 Mattias Mann is speaking

    in the Genome Sciences seminar tomorrow 11/19 at 3:30PM in the Foege auditorium.
  • Nov 17 PacMass meeting

    this Wednesday 11/19 at the Hutch.
  • Sep 25 Comet release

    2014.02 rev. 2 is now available. See release notes here.
  • Sep 18 Comet release

    2014.02 rev. 1 is now available. See release notes here.
  • Sep 16 Comet release

    2014.02 rev. 0 is now available. See release notes here.
  • Aug 09 Postdoctoral position

    in proteomics & mass spectrometry here at UW Medicine.
  • Aug 04 Job opportunity at Weill Cornell Medical College

    for a director position in a new proteomics and metabolics core.
  • Aug 01 Summer PacMass

    meeting is on Tuesday Aug 26 here at UW SLU.
  • Jul 21 Job opportunity in Dallas

    for a bioinformatics Assistant Professor.
  • Jul 18 Job opportunity in Zurich

    for a computational scientist in the Aebersold lab with long term stable funding.
  • Jun 10 TPP updated to 4.7.1

    on the UWPR systems.
  • Jun 03 Comet release

    2014.01 rev. 1 is now available. See release notes here.
  • Apr 23 Proteomics talk

    On Wed Apr 30, Brook Nunn will give a talk on oceanography proteomics in Foege Auditorium, S060, 1:30PM. Later that day at 3:30PM in the same auditorium, Steve Carr will be giving a seminar.
  • Apr 8 Proteomics talk

    Terry Farrah from ISB will be given a talk on 4/16 at 1:30PM in Foege Auditorium on using proteomics data to confirm protein coding genes and discover new protein variants.
  • Mar 25 Comet release

    2014.01 rev.0 is now available. See release notes here.
  • Mar 10 TPP updated to 4.7.0

    on the UWPR systems.
  • Feb 2 Seahawks

    are NFL Champions!
  • Jan 7 ASMS abstracts

    are due Feb 7th. Less than 2 weeks!
  • Jan 23 Comet maintenance release

    Release 2013.02 rev.2 is now available. See release notes here.
  • Jan 15 Next PacMass

    will be on Feb 15 starting at 5:30PM here at UW SLU.
  • Dec 9 US HUPO 2014

    is in Seattle April 6-9, 2014. Abstracts due Jan 31.
  • Nov 25 Comet maintenance release

    Release 2013.02 rev.1 is now available. See release notes here.
  • Nov 25 ISB TPP course in March

    Anyone interested in a TPP course, next one is being held 3/31-4/4/2014 at ISB.
  • Nov 15 Targeted Proteomics Course

    A Targeted Quantitative Proteomics course is being held by the Skyline team at the UW on 3/31-4/4/2014 which is the week before US HUPO here in Seattle. Unfortunately registration closes today.
  • Oct 21Comet 2013.02.0

    Release update for bug fix.
  • Oct 18 New Comet release

    Release 2013.02 rev.0 is now available. See release notes here.
  • Oct 14 Thai food truck at SLU

    Thai-U-Up parks here on 8th Ave. every Monday 11AM-2PM.
  • Sep 24 Shuttle service

    at SLU will be changing Oct 1st. The shuttle will leave SLU every 15 minutes (:05, :20, :35, :50) and include a FHCRC stop.
  • Jun 6 Bioinformatics positions

    are available at St. Jude Children's Research Hospital in Memphis, TN. Here's the job posting.
  • Aug 16 TPP updated

    to version 4.6.3 on UWPR systems.
  • Jul 29 Interesting article

    about balancing life and expectations for anyone considering a career in academics.
  • Jun 6 TPP updated

    to version 4.6.2 on UWPR systems.
  • Jun 5 New Comet release

    Release 2013.01 rev.0 is now available. See release notes here.
  • Jun 4 TPP Course

    ISB is holding another TPP course July 8-12 and still has spots open.
  • May 29 UWPR Seminar

    Shao-En Ong and Patrick Hutchins will speak at 4-6PM on 6/4/2013 at SLU Orin Smith Auditorium.
  • Apr 1 PacMass

    Come hear Prof. Vicki Wysocki speak at PacMass on 4/22 here at UW SLU.
  • Mar 7 Congrats

    Best wishes to Vagisha and Deepak on their new baby boy!
  • Feb 22 Comet support

    I created Comet support Google group which I'll use to post program info, give users a forum to ask questions, etc.
  • Feb 4 Comet update

    Version 2012.01 rev. 3 is released. Hopefully final maintenance release for Comet version 2012.01.
  • Jan 10 Comet update

    Version 2012.01 rev. 2 is released. Affects pep.xml output only.
  • Jan 1 Happy New Year

    The UWPR wishes that you have a great 2013!
  • Sep 19 Comet update

    Had to make a minor fix to the 2012.01.1 release of Comet to address static modifications in pep.xml output.
  • Sep 12 Comet update

    maintenance release 2012.01.1 of Comet is now available.
  • Oct 29 Updated TPP

    version 4.6.1 is now live on the UWPR system.
  • Oct 16 Congratulations

    to Eva Jahan and her husband Ethan. They had a healthy baby girl Zahra this past weekend.
  • Oct 8 UW SEQUEST update

    Version 2012.01.5 maintenance release fixes errors with the internal decoy searches. This is not being generally pushed out as we're at EOL for UW SEQUEST; if you need this update, contact me (Jimmy).
  • Sep 27 PacMass

    Dave Goodlett presets at PacMass here at SLU on Oct 4th.
  • Sep 4 UWPR Seminar

    will be held at Foege Auditorium from 4-6PM on Tues 9/11/12.
  • Aug 15 UW SEQUEST update

    Version 2012.01.4 maintenance release fixes stop codon character '*' support. This is not being generally pushed out as we're at EOL for UW SEQUEST; if you need this update, contact me (Jimmy).
  • Aug 9 SLU block party

    happening tomorrow Friday Aug 10th.
  • Aug 1 Goodlett Lab moving

    The Goodlett lab announced a move to Univ. of Maryland in Jan. 2013. The lab will be missed.
  • Jul 13 UW SEQUEST update

    Version 2012.01.3 maintenance release is live on UWPR systems. Simply adds back support for "activation_method" parameter that was broken. For mzXML inputs only.
  • Jun 21 Symposium

    The Cascadia Proteomics Symposium is being held July 19-21 at ISB.
  • Jun 20 UW SEQUEST update

    Version 2012.01.2 maintenance release is live on UWPR systems.
  • May 17 UW SEQUEST update

    Version 2012.01.1 maintenance release is live on UWPR systems.
  • Apr 24 ISB TPP course

    TPP software course is being offered by ISB on June 4-8.
  • Apr 6 New UW SEQUEST

    Version 2012.01.0 is live on UWPR systems.
  • Mar 26 Symposium

    Please join us for a one day Proteomics Symposium at the UW South Lake Union Campus preceeding Vancouver's ASMS.
  • Mar 16 TPP Update

    UWPR TPP binaries have been updated to v4.5.2 today.
  • Jan 23 Proteomics jobs

    A few UW labs are looking for good people. In this post, we're highlighting the Ong lab; go check them out!
  • Dec 22 Happy Holidays

    The UWPR wishes everyone happy holidays and a great new year!
  • Nov 17 Proteomics talk

    Come see Alexey Nesvizhskii give a talk at 11:15AM today in Foege auditorium (S060) on the topic of label-free quantitative proteomics.
  • Oct 1 UWPR Cost Center

    We're now operating as a cost center. See the Collaboration tab for info.
  • Sep 27 Informatics position

    Igenica, a biopharmaceutical company in California, is looking for a bioinformatician. Take a look at their job posting if you're interested.
  • Sep 26 Software update

    The TPP software version on UWPR cluster has been updated to recently released 4.5.0.
  • Sep 15 LTQ-FT docs

    Two new documents have been posted on our tools page covering ECD and IRMPD maintenance and optimization on an LTQ-FT Ultra. Look in the "Hardware, methods, protocols" section. Thanks Priska.
  • Sep 9 Postdoc positions

    Interested in a job in proteomics research? The Bruce lab has postdoc positions available. Take a look!
  • Sep 7 Shared Proteomics

    Check out the website which contains a wiki, forum, tutorials, etc.
  • Aug 9 Maintenance release 2011.01 rev 1 of SEQUEST

    is now available. See the release notes for a description of the updates.
  • Aug 1 8/2 UW joint proteomics group meeting is cancelled.

  • Jul 28 Next UW joint proteomics group meeting

    is 5PM this coming Tues Aug 2nd in Foege.
  • Jul 27 Sequence DB updates

    The SwissProt and human/mouse IPI databases were just updated on the Mascot server.
  • Jul 17 Food trucks at SLU

    If you're a proteomics researcher who enjoys food, visiting our SLU campus brings you close to lots of food truck options.
  • Jun 15 PacMass tomorrow

    Go see my old colleague Tim Griffin give a talk at the Hutch.
  • Jun 13 Proteomics Symposium

    The Cascade Proteomics Symposium is targeted towards a PNW audience to be held on July 17th to 19th in Seattle. See the Symposium website here for more details.
  • May 5 UW SEQUEST release

    Version 2011.01 rev 0 of UWPR Sequest has been released with minor functional updates. See the release notes here.
  • Apr 6 Pressure Cell

    Here's some info to help you setup your own packing station and pack/load columns.
  • Mar 16 Bioinformatics position in Memphis

    St. Jude Children’s Research Hospital currently has two proteomics bioinformatics positions open. If you're interested in working in Memphis, check out jobs 20477 and 20478 here.
  • Feb 7 Post doc available

    A proteomics lab here is looking for a good postdoc or two. Interested? Send in your CV and I'll pass it along. -Jimmy
  • Jan 4 Misc news

    Happy New Year and a quick note that the next joint UW proteomics lab meeting will be on Thursday January 20th at 5PM. Also belated welcome to Shao-En Ong who is a new proteomics faculty member in Pharmacology.
  • Dec 12 SAWN video

    Check out this video of surface acoustic wave nebulization being pioneered in the Goodlett lab.
  • Nov 5 Welcome Alejandro

    Dr. Alejandro Wolf-Yadlin has joined us at the UW SLU campus as a new proteomics faculty in Genome Sciences. He's looking for a post doc!
  • Nov 1 UW SEQUEST release

    A new UW-internal version of SEQUEST (version 2010.01.0) has been released. See the release notes for more information. Access to this software requires an academic use license from the UW.
  • Oct 21 Data retention policy

    Please see the new data retention policy posted on the collaboration page.
  • Sep 16 Fall PacMass meeting

    The meeting, on Wednesday October 6, will be held at the UW Medicine SLU campus in the Orin Smith Auditorium starting at 5:30PM.
  • Jun 16 Welcome Judit

    We'd like to welcome Judit Villen, new Genome Sciences proteomics faculty member, to the UW community.
  • Mar 24 ProteinCenter update

    ProteinCenter is now at v3.2. See the UWPR ProteinCenter page for details of the changes.
  • Feb 10 Power Outtage

    A major power outtage has shut down all equipment in the bulding including mass specs. It could be a few days before things are back to normal.
  • Jan 04 2010 Welcome Eva

    Eva Baker starts today at the UWPR as a software engineer.
  • Oct 12 Another triple

    A new TSQ Vantage, our second triple quad, has been installed.
  • Aug 18 new documents

    A couple of new parts lists are now available on the Tools page.
  • Jun 8 Shuttle change

    Note that due to construction, the D-wing shuttle stop has been moved to the north side of Pacific Ave NE between the two pedestrian overpasses.
  • May 25 Cluster upgrade

    22 new 8-core nodes have been added to our cluster (244 CPU cores in total) to replace retired machines.
  • Apr 28 Tesla workstation

    The UWPR has added an Nvidia workstation, including two Tescla C1060 computing processors (240 computing cores and 4GB memory each).
  • Mar 16 Goodbye Ning

    Ning Zhang has accepted a position with the UW Hospital IT group. Good luck on your new job!
  • Jan 27 2009 ProteinCenter seminar at UW

    on February 26th, 10:30AM at SLU. The is an informal seminar to learn about the functionality of ProteinCenter. It will be held in Brotman 237.
  • Dec 30 Congratulations to Mike MacCoss

    for being selected as a winner of the 2007 Presidential Early Career Award for Scientists and Engineers (PECASE). Mike is one of 12 researchers awarded the nations highest honor for scientists at the outset of their professional careers.
  • Dec 8 Welcome Jim Bruce

    The UWPR welcomes Jim Bruce, Genome Sciences proteomics faculty and our SLU co-inhabitant, to the UW proteomics community.
  • Nov 19 ProteinCenter

    UWPR researchers now have access to Proxeon's ProteinCenter software.
  • Sep 25, 2008 Local facilities

    See the link in the collaborate page to local proteomics fee-for-service facilities that may address your proteomics needs.
  • Jul 1, 2008 Welcome Ning

    We've grown by one FTE! Ning Zhang has joined our group as a software engineer; she comes from the Aebersold group at ISB.
  • Jun 3, 2008 Shuttle stop moves

    As part of the SLU campus build out progression, the shuttle stop is now on Republican St. right off the new courtyard.
  • May 19, 2008 Nanospray source

    Custom, flexible nanospray source information has been posted; check out the link in the Tools menu for detailed information.
  • Mar 4, 2008 We are hiring

    We have a position open for a Software Engineer, requisition # 41623. Here's your chance to work with great researchers and make your mark on the computational proteomics field. Related requisition #40615 closes today. Feel free to contact me with questions. -Jimmy
  • Jan 1, 2008 Happy New Year!

    We wish everyone a great 2008.
  • Dec 6, 2007 Informatics platform

    The informatics webapp adopted from the YRC is now online.
  • Oct 12, 2007 New look

    The new website has launched.