Posts in ABRF Discussion Forum

My apologies, please use the updated registration links in this email.

Welcome to September, ABRFers!  To kick off SUMS' fall seminar season this
Thursday Dr. Nick Riley, a postdoc in Carolyn Bertozzi's lab here at Stanford,
will be teaching us the fundamentals of mass spec-based glycoproteomics.  This
presentation will lay the foundation for Nick's October 1 seminar on recent
developments in glycoproteomics.  Be sure to join us for this double feature!

Special heads-up:  SUMS-RAS 2020 is approaching at light speed! Save the date
for Mass Spec: The Next Generation on Wed-Thurs October 28-29, 10am-2pm Pacific
time, to be held on your local holodeck.


Glycoproteomics seminars, Thursdays noon-1pm Pacific time:

Thursday September 3, 2020
Fundamentals: An introduction to MS-based glycoproteomics
Speaker:  Nick Riley, PhD - Dept. of Chemistry, Stanford University
register
here<https://stanford.zoom.us/webinar/register/1415954471546/WN_l-ikGrMzQtuhCknp3-bYqQ>


Thursday October 1, 2020
Reasons to be excited about current efforts in glycoproteomics
Speaker:  Nick Riley, PhD - Dept. of Chemistry, Stanford University
register
here<https://stanford.zoom.us/webinar/register/9215954473310/WN_rGnlNhoNReeDqlsTww4PVA>



Note: As many of us are getting back into the lab and our schedules are less
flexible, remember that registering for these webinars will also give you
access to the recording, to view at your convenience.

Stay safe, physically distant, and socially connected!

Best,
Allis



COVID-19 update more info<https://mass-spec.stanford.edu/covid-19>
SUMS aims to safely support the campus research restart and is operating under
Stanford's Stage 2 physical distancing rules.  Meetings and seminars continue
to be held via Zoom.

SUMS Seminar Series more info<https://mass-spec.stanford.edu/events>
Now online!  Join us via Zoom on Thursdays

____________________________________________________________

Allis Chien, Ph.D.
Director, Stanford University Mass Spectrometry


Vincent Coates Foundation Mass Spectrometry Laboratory
Stanford Cancer Institute Proteomics Shared Resource
Bass Biology Building, room 024 | 327 Campus Drive | Stanford, CA 94305

<email obscured><email obscured><email obscured>>
| 650.723.0710 | http://mass-spec.stanford.edu<http://mass-spec.stanford.edu>
____________________________________________________________

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hi there,
we are looking for good UPLC columns for glycopeptide separation, any thoughts?
thanks a lot,
xin

One of the most common questions that Core Facility (CF) staff and managers, as
well as institutional directors, ask is: “how is my CF performing?”  This
session will help CF staff by presenting case studies of evaluations, Key
Performance Indicators and multi-CF comparability studies across various
geographical regions and types of institutions.

Join colleagues from Europe and North America for this timely session.
Register here:

https://ctls-org.eu/events/september-ctls-webinar/#

We’re looking for a skilled mass spectrometrist to lead our proteomics
product development efforts at Cell Signaling Technology.  I’ve copied the
job description below.  If you or someone you know may be interested,
please contact me directly <email obscured>) or apply on this link:
https://careers-cellsignal.icims.com/jobs/1318/senior-scientist/job.



Our human resources group helps with screening, but I’ve asked them to be
sure to forward me any resumes that mention ABRF in the cover letter.  I
think this will be a fun job, with opportunities to develop methods both
for sample prep and on instrument, and good career growth opportunities.
Please let me know if you’d like any more information.

Thanks,

Kim



--
Kimberly A. Lee, Ph.D.
Director, Proteomics
Cell Signaling Technology
3 Trask Lane
Danvers, MA  01923
Office: 978-624-3205

Cell: 978-412-2300
<email obscured>

www.cellsignal.com/proteomics



*Position Summary*

CST is searching for a highly collaborative Senior Scientist to join our
Protemics team.  The successful candidate may supervise one direct report
and use his/her strong knowledge of mass spectrometry to develop methods,
analyze samples in support of all proteomics functions, and lead proteomics
product development.

*Responsibilities*

   - Design, execution, and analysis of experiments to develop, optimize,
   and qualify methods to advance CST’s proteomics capabilities
   - Collaborate closely with research and development organizations for
   LCMS analysis and data interpretation
   - Operate and maintain LCMS systems
   - Develop, test, and release proteomics products
   - Supervise research associate

*Qualifications*

   - PhD in analytical chemistry, biochemistry, or related field
   - 2+ years post-graduate experience in proteomics/mass
   spectrometry/analytical sciences
   - 4+ years on-instrument peptide LCMS experience
   - Experience with software for processing and analysis of MS data,
   including database search and quantitative and statistical analysis

Preferred Skills/Experience

   - Experience supervising one or more direct reports
   - Proven method development track record
   - Organized, logical thinker with ability to define problems, design
   studies, interpret data, and draw valid conclusions
   - Excellent oral, written, and interpersonal communication
   - Demonstrates teamwork and collaboration skills
   - High level of organization and attention to detail

--
This message contains information which may be confidential and/or
protected by attorney-client privilege.  Unless you are the addressee, you
may not use, copy or disclose to anyone this message or any information
contained in this message.  If you have received this message in error,
please send me an email and delete this message.   Thank you.

These methods may work. However, only the experiment will tell if they work for
your collagen sample.

Deglycosylation of proteins in Clostridium spore appendages (newer method).

Twenty microlitres of appendages was lyophilized in 5 mm (outside diameter) ¥
50 mm borosilicate glass tubes in a SpeedVac for 2 h, mixed with 25 ml
trifluoromethane sulphonic acid for 60 min at 0°C (Tams and Welinder, 1995), and
neutralized with 75 ml of 60% pyridine in water in a dry ice – methanol bath.
Deglycosylated proteins were precipitated by methanol-chloroform (Wessel and
Flügge, 1984).To 100 ul of sample, 400 ul of methanol, 300 ul of chloroform and
400 ul of water were added and mixed thoroughly and centrifuged at 9000 rpm for
20 min at room temperature. The protein precipitated at the interface and the
upper phase was carefully discarded. Three hundred microlitres of methanol was
added and centrifuged as above. The liquid was discarded, and the pelleted
precipitate was dried in a SpeedVac and dissolved in native buffer.

The pellet can be used for analysis via gel-electrophoreses, Edman sequencing,
or proteomic analysis.

Walker et al. ; Molecular Microbiology 2007, 63(3), 629-643.

Deglycosylation of proteins in Clostridium spore appendages (older method).

For determination of sugars, appendages were hydrolyzed for 4 hr at 100 C with
2.4 ml of 2 N H2SO4 in sealed glass tubes. The H2SO4 was then neutralized with
concentrated Ba(OH)2, and the precipitated BaSO4 was removed by centrifugation.
The total carbohydrate content of appendage hydrolysates was determined by the
phenol-sulfuric acid method of Dubois et al. (2). Glucosamine does not react in
this test. To separate the sugars, two-dimensional descending paper
chromatography was conducted on Whatman no. 1 paper with n-butanolacetic
acid-water (BAW, 60:10:20, v/v) as the first solvent, and 2,6-lutidine-water
(LW, 65:35, v/v) as the second solvent. Sugar spots were located with acid
aniline phthalate reagent. The presence of glucose was confirmed, and the
amount was estimated by the Glucostat Reagent (glucose oxidase, Worthington
Biochemical Corp.).

Ref.: Yolton et al. 1972 Journal of Bacteriology, p 881-885.

For this method, if the deglycosylated protein is not soluble and in the
supernatant, purification can be tricky.

Good luck.

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of Kym Faull
Sent: Friday, August 21, 2020 3:54 PM
To: <email obscured>
Subject: Re: [ABRF Discussion Forum] Advice about deglycosylating collagen (and
other proteins)

I forgot to mention that collagen is naturally glycosylated on lysine and
hydroxylysine residues.

> On Aug 21, 2020, at 1:52 PM, Kym Faull <email obscured>> wrote:
>
> Does anyone have advice on ways to deglycosylate collagen (and other
proteins).  What is the most effective method?  Any and all advice will be
appreciated.
>
> Kym
>
>
> Kym Francis Faull, Ph.D.
> Director, Pasarow Mass Spectrometry Laboratory Jane and Terry Semel
> Institute for Neuroscience and Human Behavior at UCLA Professor
> Emeritus, Department of Psychiatry and Biobehavioral Sciences David
> Geffen School of Medicine at UCLA
> Telephone: (310) 206 7881 (office)
> Telephone: (310) 206 7886 (laboratory)
> Facsimile: (310) 206 2161
> Electronic mail: <email obscured> <email obscured>>
>
>
>
>
>
>
>
>
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Does anyone have advice on ways to deglycosylate collagen (and other proteins).
What is the most effective method?  Any and all advice will be appreciated.

Kym


Kym Francis Faull, Ph.D.
Director, Pasarow Mass Spectrometry Laboratory
Jane and Terry Semel Institute for Neuroscience and Human Behavior at UCLA
Professor Emeritus, Department of Psychiatry and Biobehavioral Sciences
David Geffen School of Medicine at UCLA
Telephone: (310) 206 7881 (office)
Telephone: (310) 206 7886 (laboratory)
Facsimile: (310) 206 2161
Electronic mail: <email obscured> <email obscured>>

All,
I have been trying to get involved with the new faculty onboarding process.
There is an orientation day part of which consists of visiting a "fair" with
booths in a huge room. All sorts of things are represented - things that might
be of interest to new faculty. I am a one core director (EM) but for various
reasons I have involvement with all cores. I have wanted to have a booth for
core facilities. I have thought of having one page flyers for each core at the
booth but to have the booth staffed at all times. It would need to be someone
with at least a passing knowledge of all cores and also some knowledge of iLab
for which we have a site license. I think there are too many core facilities to
have a booth for each one. One day I will volunteer to the right person and
have my idea turn into practice - I hope!

​​​​​
Chris
He/Him/His
Christopher J. Gilpin Ph.D.
Campus-wide Coordinator for Electron Microscopy
Director, Life Science Microscopy Facility
Purdue University
Whistler Hall of Agriculture Research, Room S052
170 S. University St
West Lafayette, IN 47907
765-494-7750
<email obscured>
<email obscured> reaches everyone in the facility.
http://ag.purdue.edu/arp/Microscopy/Pages/default.aspx
skype cjgilpin

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of
<email obscured>
Sent: Wednesday, August 19, 2020 8:43 AM
To: <email obscured>
Subject: Re: [ABRF Discussion Forum] Onboarding Process for New PI's,
Scientists

To be honest Andy,  when a bunch of information is piled on me I never remember
everything, but rather hold to how to get the information when I need it and
some broad brush strokes of what was communicated.

I think it is human nature to only pay attention to every detail when we not
are going to use something in the immediate future.  A solution I really like
is to have next best thing to concierge service (a cheaper) a simple internal
"core listserv / PDL" to which PI/Postdocs/student/tech can asks all the cores
at once.  Sends a post asking if anyone provides X service, has Y instrument or
can help them accomplish Z (for when they do not know what could address their
technical challenge).  This would be a constant to a quick overview of what it
offer, ideally with time for them to ask thing of specific interest to them
when they are just getting set up.  A "Technical Expertise Listserv" has 2 main
benefits ...

(1) helps labs connect with cores rather than asking around, which is hit or
miss, or looking on the websites never as easy as one would think ...

(2) also allows the cores / institution to know in real time what is needed
because researchers would be telling.

It is a cheap solution that I have always wanted to have in place, but it is
above my pay grade.

Good Luck.

Frances

ZRC 1563
Office     646-888-2354
Mobile   516-967-0656


On 8/14/20, 6:10 PM, "ABRF Discussion Forum on behalf of chitty"
<email obscured> on behalf of <email obscured>> wrote:

    Hello,

    OHSU is exploring ways that we can improve the onboarding process for
newcomers to our community. Although this is proposed as a project for the
entire research enterprise, I am helping to lead it because our cores are
specifically interested in making sure they are included in the PI and new
scientist onboarding process.

    Although there are some onboarding processes in place, they tend to be
department specific or program specific. Newcomers sometimes have to find their
way to cores and other services by doing their own research. Do any
institutions have onboarding models and processes that are a bit more inclusive
and consistent including various groups and services throughout the research
community? It would be great to hear from you if you have information you are
willing to share.

    Thanks!
    Andy Chitty
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To be honest Andy,  when a bunch of information is piled on me I never remember
everything, but rather hold to how to get the information when I need it and
some broad brush strokes of what was communicated.

I think it is human nature to only pay attention to every detail when we not
are going to use something in the immediate future.  A solution I really like
is to have next best thing to concierge service (a cheaper) a simple internal
"core listserv / PDL" to which PI/Postdocs/student/tech can asks all the cores
at once.  Sends a post asking if anyone provides X service, has Y instrument or
can help them accomplish Z (for when they do not know what could address their
technical challenge).  This would be a constant to a quick overview of what it
offer, ideally with time for them to ask thing of specific interest to them
when they are just getting set up.  A "Technical Expertise Listserv" has 2 main
benefits ...

(1) helps labs connect with cores rather than asking around, which is hit or
miss, or looking on the websites never as easy as one would think ...

(2) also allows the cores / institution to know in real time what is needed
because researchers would be telling.

It is a cheap solution that I have always wanted to have in place, but it is
above my pay grade.

Good Luck.

Frances

ZRC 1563
Office     646-888-2354
Mobile   516-967-0656


On 8/14/20, 6:10 PM, "ABRF Discussion Forum on behalf of chitty"
<email obscured> on behalf of <email obscured>> wrote:

    Hello,

    OHSU is exploring ways that we can improve the onboarding process for
newcomers to our community. Although this is proposed as a project for the
entire research enterprise, I am helping to lead it because our cores are
specifically interested in making sure they are included in the PI and new
scientist onboarding process.

    Although there are some onboarding processes in place, they tend to be
department specific or program specific. Newcomers sometimes have to find their
way to cores and other services by doing their own research. Do any
institutions have onboarding models and processes that are a bit more inclusive
and consistent including various groups and services throughout the research
community? It would be great to hear from you if you have information you are
willing to share.

    Thanks!
    Andy Chitty
    ――
    View topic http://list.abrf.org/r/topic/3WjBexNi5tFxqSHjmMIYSX
    Leave group <email obscured>?Subject=Unsubscribe




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<email obscured> ***

=====================================================================

     Please note that this e-mail and any files transmitted from
     Memorial Sloan Kettering Cancer Center may be privileged, confidential,
     and protected from disclosure under applicable law. If the reader of
     this message is not the intended recipient, or an employee or agent
     responsible for delivering this message to the intended recipient,
     you are hereby notified that any reading, dissemination, distribution,
     copying, or other use of this communication or any of its attachments
     is strictly prohibited.  If you have received this communication in
     error, please notify the sender immediately by replying to this message
     and deleting this message, any attachments, and all copies and backups
     from your computer.

Hi,
The registration link for this doesn't go the usual name address etc; it
doesn't seem to be working.


Best regards,
Margaret Coe
Technologist
Equity chair
Liggins Institute
University of Auckland

+64 9 923 3432

________________________________________
From: ABRF Discussion Forum <email obscured>> on behalf of GroupServer
Administrator <email obscured>>
Sent: Tuesday, 18 August 2020 5:07 a.m.
To: <email obscured>
Subject: [ABRF Discussion Forum] MWACD Presentation: SYSTEMIC RACISM IN STEM
AND CONSIDERATIONS FOR SHARED RESOURCE FACILITIES

SEPTEMBER 1, 2020
2:30-4:00 PM ET

Panelists:
Laura Martin, PhD, University of Kansas Medical Center
Vernadette Simon, MS, Mayo Clinic
Donald Warne, MD, MPH, University of North Dakota

Moderator:
Mary Winn, PhD, Van Andel Institute

Register:
https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmwacd.org%2Fsystemic-racism-panel&amp;data=02%7C01%7C%7C1b345a00f9c94a9fd60c08d842d018a4%7Cd1b36e950d5042e9958fb63fa906beaa%7C0%7C0%7C637332809560736389&amp;sdata=FTWWjPsEr6HXetY%2BWOqeeC1nRr9VGby%2Bvh4zpDucUzs%3D&amp;reserved=0
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Wednesday, September 30, 1:00 pm ET

Aimed at helping scientists and core administrators learn more about how to
express their goals, needs and interests.  Bridging these Communications gaps
can be an important way to improve the effectiveness and value of core
facilities. Chris Dillon with the University of Florida will moderate the
discussion.

Register here:
https://us02web.zoom.us/meeting/register/tZctdOysqjosHdbuPgNHv6cIrS2zL_fAFVzw