Proteome Software Newsletter Archive

The following document provides links to older newsletters.

Newsletter 28 - Spring 2019: Volume 11, Issue 3

The 2019 Scaffold User Group Meeting will take place before the ASMS annual conference on Sunday, June 2, 2019. We look forward to seeing everyone who registered at the Westin Peachtree Plaza, Chastain E Ballroom.

Newsletter 27 - Early Spring 2019: Volume 11, Issue 2

Notes on Scaffold User's Group Meeting, ASMS 2019, Updates from Development, and the Scaffold Publication Spotlight. Lots of exciting news this year!

Newsletter 26 - Winter 2019: Volume 11, Issue 1

Scaffold Elements Featured in Journal of Proteome Research Article. The article was recently published in the Software Tools and Resources issue, and highlights our novel algorithm for improving identification rates by matching in-source fragments to fragments found in MS/MS spectral libraries, even when no MS2s were captured. Click on the image below to view the flyer, with a link to the paper.

Newsletter 25 - Late Summer 2018: Volume 10, Issue 6

Proteome Software encourages those interested to participate in the 2018 ABRF PRG study "Evaluation of Data-Independent Acquisition (DIA) for Protein Quantification in Academic and Core Facility Settings". The study this year will focus developing best practices for DIA proteomics in regards to sample processing, data acquisition, and data analysis. All participants are eligible for an extended evaluation of Scaffold DIA.

Newsletter 24 - Summer 2018: Volume 10, Issue 5

We welcome everyone to sign up for our User Group meeting, preceding the annual ASMS conference, on Sunday, June 3, 2018 from 2:00 to 5:00 PM. The meeting will take place in the Cortez C Ballroom at the Kimpton Solamar Hotel in San Diego, California. Click on the button below to register.

Newsletter 23 - Early Summer 2018: Volume 10, Issue 4

The conference season has already begun and Proteome Software has been represented at both US HUPO and ABRF. Please join us at ASMS booth 314 in June and World HUPO in October. Scaffold DIA is now available for evaluation!

Newsletter 22 - Spring 2018: Volume 10, Issue 3

Proteome Software will be attending the ABRF annual meeting from April 22-25 in Myrtle Beach, SC. Check us out at booth 408!

Newsletter 21 - Early Spring 2018: Volume 10, Issue 2

After the announcement at ASMS 2017, we are proud to officially release Scaffold DIA. Proteome Software hopes to keep up with current trends by expanding our product line to include Data-Independent Acquisition proteomics. Existing Scaffold users will recognize the same user-friendly interface that has come to be the industry standard for visualizing proteomics data.

Newsletter 20 - Winter 2018: Volume 10, Issue 1

Happy New Year from all of us at Proteome Software. We have a big year planned, so take a read and get in touch.

Newsletter 19 - Fall 2017: Volume 9, Issue 4

With another year speeding to its end, please take a minute to enjoy our Fall newsletter. We are gearing up for the release of our new product, Scaffold DIA, and we will be integrating the Metlin library into Elements.

Newsletter 18 - Summer 2017: Volume 9, Issue 3

With another year’s ASMS over, it is time for an update from Proteome Software. Thank you to all who attended our User Group meeting or stopped by our booth. The conference this year was exhausting, informative, fun and we got a lot of great feedback from our users that we hope to incorporate into future releases.

Newsletter 17 - Spring/Summer 2017: Volume 9, Issue 2

Come see us at ASMS this year, June 4th - 8th, booth #218

Newsletter 16 - Spring 2017: Volume 9, Issue 1

We hope to see you this years ASMS conference in Indianapolis, IN from June 4th through June 8th. Our users group meeting will take place on Sunday June 4th at 2:00 PM at the Hyatt Regency in Studio One (3rd floor). We can also be found at both #218 in the exhibition hall.

Newsletter 15 - Spring 2016: Volume 8, Issue 1

We hope you will join us at the ASMS meetings next month in San Antonio. You can find us at Booth #322 in the exhibition hall and on Sunday, June 5th, at our Users Group Meeting in Room 005

Newsletter 14 - Summer 2015: Volume 7, Issue 3

Proteome Software has release our new metabolomics MS search application: Elements for Metabolomics

Newsletter 13 - Spring 2015: Volume 7, Issue 2

Proteome Software, the maker of Scaffold, will be exhibiting in booth #31 at ASMS. We'll be showcasing our new Elements software for metabolomics. Join us at our Scaffold User Group Meeting

Newsletter 12 - Spring 2015: Volume 7, Issue 1

Come see us this year at ABRF, MSACL, ASMS and Metabolomics 2015. Scaffold has been updated to support more file formats including AB SCIEX Protein Pilot 5.0, Agilent Spectrum Mill mzXML and more. The Quantify View has been enhanced with multiple features including a Volcano Plot. Scaffold perSPECtives has new features including FDR thresholding and protein grouping during loading, allowing users to set default parameters. Learn more about Elements for Metabolomics. We will be giving demos of this new product, now in beta testing.

Newsletter 11 - Summer 2014: Volume 6, Issue 2

Come see us at ASMS this year. Sneak peak at our new metabolomics product, Elements, for Metabolomics. Scaffold perSPECtives has new features, including label free quantitation and an interactive heatmap.

Newsletter 10 - Spring 2014: Volume 6, Issue 1

Come see us at ABRF, US HUPO and ASMS this year. Scaffold, Q+ and Q+S have been updated and released with many new features. Q+ and Q+S now support iTRAQ and TMT data from MaxQuant. Additionally, TMT 10-plex and 8-plex are supported as well as dimethyl quantitation from MaxQuant and Proteome Discoverer.

Newsletter 09 - Fall 2013: Volume 5, Issue 3

Come see us at HUPO in Japan, booth #42. Plus, we launched a new product, perSPECtives, that allows flexible analysis and organization of large-scale proteomics experiments, with robust, iterative filtering to find proteins of interest. Adaptive differential expression coloring to make changes pop.

Newsletter 08 - Summer 2013: Volume 5, Issue 2

Come see us at ASMS at booth #62. Plus, User's Group Meeting on Sunday, June 9th, 2013, 230pm. Our flagship product, Scaffold 4 is stable at 4.0.5. New FDR filtering, GO Term comparison by category, more robust statistics and compatibility with MaxQuant label-free quantitation.

Newsletter 07 - Spring 2012: Volume 5, Issue 1

Our flagship product, Scaffold 4 has been released! New FDR filtering, GO Term comparison by category, more robust statistics and compatibility with MaxQuant label-free quantitation.

Newsletter 06 - Fall 2012: Volume 4, Issue 2

How to queue structured directories for easily loading complex experiments that have multiple categories and biosamples; ASMS presentation describing non-parametric statistical methods used in Scaffold Q+ and Scaffold Q+S; User Group presentation about Scaffold PTM 2.0 features such as global motif analysis, quantification at modification sites and localization filtering; Proteome Software is distributing Mascot Distiller in the USA; Scaffold supports Spectrum Mill files; an early look at Scaffold 4.0; Scaffold Suite feature comparison table

Newsletter 05 - Spring 2012: Volume 4, Issue 1

SILAC quantitation with Scaffold Q+S; enhanced statistics in Scaffold Q+; computer memory settings for improved speed; what are Progenesis LC-MS and HDExaminer?

Newsletter 04 - Fall 2011: Volume 3, Issue 2

MassQC standalone; custom gene ontology annotations; Scaffold reads Proteome Discoverer MSF files; enhanced Scaffold Batch features; computer memory settings for improved speed; Scaffold PTM batch; we distribute Sierra Analytics HDExaminer

Newsletter 03 - Winter 2011: Volume 3, Issue 1

MassQC standalone; grouping algorithm explained; configuring protein annotation preferences; label-free quantitation with Progenesis LC-MS; Scaffold Batch

Newsletter 02 - Winter 2010: Volume 2, Issue 1

The what, why, how of MassQC! Learn about LC-MS quality control in the field of proteomics. System variability, instrument performance and more...

Newsletter 01 - Winter 2009: Volume 1, Issue 1

Create reverse FASTA databases; MassQC is coming; journal article on the importance of correct peptides and proteins in complex mixtures; Scaffold Q+ is launched; downloading GOA database; Scaffold Batch

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