PEAKS Studio 7.5

We are excited to announce the release of PEAKS Studio 7.5. There are many new features in this release that expand the capabilities for our users. Just to name a few favourites, consider:

• PEAKS PTM Profiling – to detect and quantify modifications
• Peptide Mapping - a powerful comparison tool, providing an intensity map of all the peptides associated with any particular protein.
• Peptide Feature Intensity – in one click users can analyze and quantitative peptides across all samples.
• Automated Multi-Round Search – automatically filter out high quality spectra unmatched after database searching perform additional searches against different sequence databases or change parameter settings to help explain more from your data.

These were designed to further compliment PEAKS’ proven track record of high accuracy and high sensitivity in third party studies. A complete list of improvements and additions to the software can be found here: PEAKS Studio 7.5.

ASMS 2015

The expanding popularity of PEAKS made for another exciting ASMS annual conference. During the PEAKS Meeting on Sunday, BSI gave an early glimpse into a future version of PEAKS Studio. Guest speakers also presented current research projects where PEAKS proved vital:

• Jeanne Rumsey of Washington University in St. Louis,
• Database Search Strategies for Biomarker Design in Infectious Diseases

• Dr. Cheryl Lichti, University of Texas Medical Branch,
• PEAKS and the Quest for Single Amino Acid Variants

During the conference a number of notable oral presentations and posters resonated well with attendees and emerging methods. (Please note you will need to login using your ASMS details to view the presentations.)

• Ming Yao, Bristol-Myers Squibb
• Untargeted and Rapid Detection and Characterization of Modified Monoclonal Antibodies using LC-TripleTOF and Multivariate Statistical Analysis,(Slides)

• Josh Elias, Stanford University
• Fast and Accurate Unrestricted Spectrum Interpretation: You Don’t Know What You’re Missing.

A significant list of oral presentations and posters relevant to PEAKS users are available on our ASMS 2015 webpage. Our own poster, Peptide Mapping for Quantitative Profiling of Peptide Variants using PEAKS is also available.

ABRF iPRG 2015

The purpose of this year’s ABRF iPRG study was to evaluate different data analysis methods for relative protein-level quantification in label-free proteomics. In conclusion of the study, PEAKS label-free quantification proved to successfully demonstrate a high-level of accuracy in determining relative protein abundance.

 

Graphs from the results were retrieved from the ABRF iPRG Preliminary Results Summary. To view the full Preliminary Results Summary, please use the link provided below.

 

The first graph shown is an overview of all the participating Study IDs in relation to their results as seen on slide 20 in the Preliminary Results Summary. The same graph is then presented again on slides 24 and 25 (zoomed in), to show the specific tools used for peptide ID, as well as quantification for each submission. .

 

Of the 51 submissions, very few were able to recognize the true differentially abundant (DA) proteins, as seen in the graph. PEAKS, however, recognized all 6 true DA proteins (represented in blue), and reported 0 false DA proteins (represented in red).

 

 

http://www.abrf.org/ResearchGroups/ProteomicsInformaticsResearchGroup/Studies/vitek-iPRG15.pdf

 

 

Participating researchers were required to detect and identify proteins that changed in relative abundance among four biological samples, prepared from the same S. cerevisae yeast cell lysate.

 

To truly focus on the statistical assessment of the varying data processing approaches, the peptide identifications and their associated integrated peak intensities were provided to all participants.

PEAKS in Germany: Proteomic Forum 2015

Come by and visit PEAKS at this year's DGPF: Proteomic Forum (booth 19). The conference will be taking place March 22-25 at the Technical University Berlin (Germany).

In addition, PEAKS will be hosting a Training Workshop, March 19-20, 2015, at the Crowne Plaza, Berlin City Center. The workshop is designed to give users a hands-on approach to fully understanding the capability of PEAKS. Visit http://www.bioinfor.com/ for more information and registration.

“The German Society of Proteomic Research coordinates and provides a network comprising academic institutions, commercial companies and special institutions at the national and international level in order to support the extension of scientific knowledge in the field of proteome research and protein analysis.”

For more information, visit http://www.proteomic-forum.de/

PEAKS at US HUPO 2015

Stop by Booth 11 to visit PEAKS at the 11th annual US HUPO Conference. This year’s conference, located in Tempe, AZ, will span three days and include the research poster “Quantitative Analysis of Native Peptides with LC-MS/MS Directly from Complex Secretome Samples” in Computational Methods and Statistics.

From live demos to direct support, we want to show you why PEAKS is right for your research.

“US HUPO is a non-profit educational and networking association for those engaged in proteomics technologies and research pertaining to the human proteome and model organisms.”

Analysis of histone modifications with PEAKS 7

The complex nature of histone modification patterns has posed as a challenge for bioinformatics analysis over the years. Yuan et al. [1] conducted a study using two datasets from human HeLa histone samples, to benchmark the performance of current proteomic search engines. This article was published in J Proteome Res. 2014 Aug 28 (PubMed), and the data from the two datasets, HCD_Histone and CID_Histone (PXD001118), was made publically available through ProteomeXchange. With this data, the article uses eight different proteomic search engines to compare and evaluate the performance and capability of each. The evaluated search engines in this study are: pFind, Mascot, SEQUEST, ProteinPilot, PEAKS 6, OMSSA, TPP and MaxQuant. 

 

In this study, PEAKS 6 was used to compare the performance capabilities between search engines. However, PEAKS 7, which was released November 2013, is the latest version available of the PEAKS Studio software. PEAKS 7 not only includes better performance than PEAKS 6, but a lot of additional and improved features. Our team has reanalyzed the two datasets HCD_Histone and CID_Histone with PEAKS 7 to update the ID results presented in the publication by Yuan et al.  These updated results showed that instead, it is PEAKS, pFind and Mascot that identify the most confident results.

 

Proportion of Confident IDs

As indicated in the article, the two HeLa histone datasets were examined by each search engine using the same database search parameters. Seven variable modifications of histone were used in the study, and are reiterated in table 1 below.

 

Table 1. Modification parameters for database search

Fixed modification	Propionyl[Peptide N-term]/+56.02
Variable modification	First (un)	Propionyl[K]/+56.026
	Second (ac)	Propionyl[K]/+56.026; Acetyl[K]/+42.011
	Third (me)	Propionyl[K]/+56.026; Methyl_Propionyl[K]/+70.042
	Fourth (di)	Propionyl[K]/+56.026; Dimethyl[K]/+28.031
	Fifth (tr)	Propionyl[K]/+56.026; Trimethyl[K]/+42.047
	Sixth (ph)	Propionyl[K]/+56.026; Phospho[ST]/+79.966
	Seventh (co)	Propionyl[K]/+56.026; Acetyl[K]/+42.011; Methyl_Propionyl[K]/+70.042; Dimethyl[K]/+28.031; Trimethyl[K]/+42.047; Phospho[ST]/+79.966

 

When the data was run with PEAKS 7 also using these same parameters, an updated comparison of the IDs and confident IDs from the article published by Yuan et al. was created, as shown in figure 1. The comparison includes the results produced by the eight different search engines. IDs (shown as solid bars) from each search engine are identifications with an FDR < 1%; whereas confident IDs (shown as striped bars) are the number of IDs from each search engine which are also present in the ‘all_Confident’ group of IDs. The term ‘all_Confident’ was used to indicate IDs that were found by at least two of the eight different search engines.

Figure 1 (a-g). Comparison of the number of IDs and confident IDs of the seven variable modifications produced by the different search engines using HeLa histone HCD and CID data

(a) indicates the number of first (un) modified ID; (b) number of second (ac) modified ID; (c) number of third (me) modified ID; (d) number of fourth (di) modified ID; (e) number of fifth (tr) modified ID; (f) number of sixth (ph) modified ID; and (g) number of seventh (co) modified ID.

By analyzing each of the graphs presented in figure 1, PEAKS 7 produces the most confident results of the search engines evaluated in the study, along with pFind and Mascot. This is true in all cases (un, ac, di, tr, ph, and co; where ph tied with pFind and Mascot, and co tied for first with Mascot) except in the third modification where pFind and Mascot found the most confident result. 

Running Time
 

For this analysis, PEAKS 7 was run on a typical desktop computer with an i7 CPU and 16G RAM.  PEAKS 7 finished each of the first six searches (un, ac, me, di, tr, and ph) around 22 minutes and then 14 minutes for the HCD_Histone and CID_Histone database searches respectively.  Compared to 2h-7h indicated by [1] using PEAKS 6, the speed of PEAKS 7 is much faster. For the seventh search which involved multiple PTMs (co), PEAKS spent 30 minutes, and then 14 minutes performing the database search for HCD_Histone and CID_Histone respectively.

Therefore, the performance time of PEAKS 7 is very comparable to the other search engines as drawn in conclusion from [1] and consistent with the performance capabilities presented in (http://peaksblog.bioinfor.com/2013/12/boost-your-analysis-speed-with-peaks-7.html).

References

1.     Yuan ZF, Lin S, Molden RC, Garcia BA. Evaluation of proteomic search engines for the analysis of histone modifications.  J Proteome Res. 2014 Aug 28. [Epub ahead of print]

 

PEAKS Training and Workshop, September 1-3, 2014 – Paris, France

PEAKS will be in Paris, France hosting both a training course and a workshop starting this September.

A two-day PEAKS training course and a one-day workshop will be held at the Hotel Paris Bastille located at 67 rue de Lyon, Paris France.

The training course is designed to introduce users to the software, and elevate their understanding to become a confident user. Attendees will gain hands-on data analysis experience with PEAKS from the people who develop and support it.

The workshop is designed for participants facing more difficult challenges in their research. This hands-on PEAKS practice will definitely increase your expertise of LC-MS/MS data analysis and quality control.

More details can be found here. You can also register here directly.