R

C o m p l e t e S o l u ti o n f o r P r o t e o m i c s

Generate highly accurate and sensitive results from large-scalestudies

TMT/iTRAQ • SILAC • Label-free

Acquire more confident results from complex biological samples without sacrificing precision

Database Search • De novo Sequencing • PTM Search • Homology Search

www.bioinfor.com

> MultiNotch MS3 quantification supported.

> Supports larger-scale and cross-experiment with TMT/iTRAQ and SILAC.

> Both labelled and label-free quantification are supported with protein FDR estimation.

> Feature-based SILAC quantification module including correction of Arginine to Proline conversion.

> Supports searching a target database together with a contaminant database.

> Displays protein sequence coverage in enzyme-specific format.

> Lock mass calibration support for Waters data.

Version Highlights:

The newest addition to the PEAKS Software SuiteR

Complete Solution for Proteomics

Label free, SILAC, TMT/iTRAQ protein quantification

Robust quantitation and statistical analyses

> SILAC, TMT/iTRAQ, Label-free and other similar methods are all supported by PEAKS. As your lab’s needs evolve, you have flexibility in your quantification method.

> Cutting edge quantification techniques and standard statistical analyses, such as Benjamin and Hochberg FDR and ANOVA significance, are automatically performed and presented in an intuitive interface.

Differentially expressed proteins highlighted with confidence > Heat map clearly gives you the proteins showing significant change between conditions, cutting hours out of analysis time.

for QuantificationR

WT 1

WT 2

WT 3

SMA1

SMA2

SMA3

Wild typeSevere SMA

log2(Ratio)Q8VEH3|ARl8A_MOUSEQ6IFZ6|K2C1B_MOUSEP19324|SERPH_MOUSEP16015|CAH3_MOUSEA2ABU4|MYOM3_MOUSEQ9CPR4|RL17_MOUSEP62631|EF1A2_MOUSEQ01405|SC23A_MOUSEQ61425|HCDH_MOUSEQ9DBC7|KAP0_MOUSEQ61584|FXR1_MOUSEQ8VDM4|PSMD2_MOUSEP23116|EIF3A_MOUSEP53026|RL10A_MOUSEQ80X19|C0EA1_MOUSEP35550|FBRL_MOUSEP62245|RS15A_MOUSEQ03265|ATPA_MOUSEQ9JI91|ACTN2_MOUSEQ61553|FSCN1_MOUSEP45376|ALDR_MOUSEP14685|PSMD3_MOUSEQ8BTM8|FLNA_MOUSEP02772|FETA_MOUSEQ8TQI3|OTUB1_MOUSEO70400|PDLI1_MOUSEP47963|RL13_MOUSEQ5U405|TMPSD_MOUSEP99024|TBB5_MOUSEP09528|FRIH_MOUSEQ60932|VDAC1_MOUSEP06151|LDHA_MOUSEQ9CQ69|QCRS_MOUSEQ9CR21|ACPM_MOUSEQ61937|NPM_MOUSEQ60930|VDAC2_MOUSEP19783|COX41_MOUSEQ9CPQ|COX6C_MOUSEP00405|COX2_MOUSEP56382|ATP5E_MOUSE

> Define your replicates and conditions at the channel and sample level; have complete control over result presentation.

Take control with experiment setting features

Sign

ifica

nce

Ratio

> MultiNotch MS3 quantification supported.

> Supports larger-scale and cross-experiment with TMT/iTRAQ and SILAC.

> Both labelled and label-free quantification are supported with protein FDR estimation.

> Feature-based SILAC quantification module including correction of Arginine to Proline conversion.

> Supports searching a target database together with a contaminant database.

> Displays protein sequence coverage in enzyme-specific format.

> Lock mass calibration support for Waters data.

www.bioinfor.com

> For large-scale, protein quantification studies, you can now expand your sample size with reference channels to enhance the accuracy of quantification.

Combining experiments with reference channels

for TMT/iTRAQR

Accurate and sensitive quantification > MultiNotch MS3 approach removes interference signals from co-isolated species; thus, providing high-quality quantification results.

Observe and validate with ease > Validate the significant changes seen in the heat map by assessing individual intuitive significance and quality scores. Cut hours out of analysis time and make filtering out false positives easy. These changes filter downstream and will automatically be reflected in the heat map and other PEAKS-based quantification results.

Experimental Design

PEAKS Results

Arginine to Proline Conversion Correction

Intuitive interface showing paired features at a glance > Visualize the raw data in a 3D LC/MS heat map and an extracted ion chromatogram for easy result validation.

Complete Solution for Proteomics

Unsurpassed sensitivity of peptide feature detection > PEAKS uses a novel peptide feature detection algorithm to find peptide feature pairs. You can now minimize the biases from missing values.

> Software correction of arginine to proline conversion improves the accuracy.

for SILACR

www.bioinfor.com

PEAKS DB maximizes sensitivity and accuracy of protein and peptide identification

for Protein IDR

> The unique method of incorporating de novo sequencing into a database search allows for an enhanced separation of true and false hits. You will identify more peptides and proteins with greater confidence.

Intuitive coverage view gives full control > The fully interactive coverage view allows you to dive deeper into the results. Interrogate the statistics behind individual peptide hits or inspect individual peptide-spectrum matches.

Easy result filtering > With a few clicks, you can specify a false discovery rate and customize result filters. Quickly define and visualize your confident results.

All Spectra

DB Peptides Novel Peptides

DB Search De Novo

Found?No

Yes

Maximize your modified peptide identifications with PEAKS PTM

for PTMs and MutationsR

> Protein identification designed for PTMs and mutations. PEAKS PTM allows you to search all the naturally occurring modifications found in the Unimod database at once.

Find mutated peptides with SPIDER > Find confident hits that are different from the database entry with our de novo- tailored homology search. SPIDER uses a novel method to find peptides with single amino acid variants.

Unified scoring for easy interpretation > PEAKS DB, PEAKS PTM, and SPIDER results are all scored using -10lgP. So, results from the three algorithms can be displayed together on the same scale.

Complete Solution for Proteomics

Raw MS data

De novo seq.

PEAKS DB

PEAKS PTM

SPIDER

Novel Peptides

DB Peptides

PTMs

Mutations

3,7-Phospho 5,7-Phospho

DISLSDYK

www.bioinfor.com

PEAKS de novo peptide sequencing is world renowned and the base of all PEAKS analysis > The PEAKS unique de novo sequencing algorithm accurately predicts a peptide sequence without the use of a database. The sequences are then used to enhance PEAKS DB, PEAKS PTM, and SPIDER analyses.

for De NovoR

Accuracy at the amino acid level > Local confidence scores are assigned for each amino acid. You can easily separate confident amino acid assignments from false positives.

Find novel peptides not recorded in protein databases > De novo results from scans missed in protein databases are summarized in ‘de novo only’ results. Partial protein matches or “de novo tags” are also given and can be viewed directly from the coverage pane.

The fragment score calculation only requires the prefix mass; thus, it is possible to define score f(m) for eachprefix mass value m

Peptide

Prefix Suffix

Novel Peptide Candidates

Service Plan Subscription R

Receive first in class customer serviceOur Service Plan Subscription (SPS) connects you with our experienced staff seamlessly. Take advantage of our expertise, and receive unlimited Application and Technical Support with PEAKS.

It’s cheaper to stay currentDon’t let your subscription expire! With a current SPS receive the most cost savings when signing a subscription for another year (or more).

Free year of SPS for all new customersLet the value of SPS speak for itself and receive the benefits of SPS for free for all new purchases. We believe after experiencing our support firsthand, you will see a large difference compared to industry standards. At only 30% of the list price, institutions can not only access the support their research deserves but also get access to the latest version annually.

Complete Solution for Proteomics

A software tool that grows with your researchStay ahead of the competition. Pushing the envelope means tackling today’s toughest problems with current knowledge and tools. Keep your skills and tools up-to-date by subscribing to BSI’s service plan. With an active SPS, receive the latest version of PEAKS, patch updates, and custom tools at no additional cost.

Learn More:www.bioinfor.com

Telephone Number:1-(855) 885-8288

Pricing Request:sales@bioinfor.com

Support Inquiries:support@bioinfor.com

SEQ Automated antibody protein sequencing with LC-MS/MS.

Antibody protein sequence validation.

Qualitative and quantitative analysis of PTMs and sequence variants.

Assessment of impurities.

Comprehensive and automated report generation.

Antibody Characterization Software

From Service to Software tool, PEAKS AB, for all your therapeutic protein characterization needs

Trust Our Service

Enjoy Our Software

Full sequence coverage and 100% accuracy guaranteed.

Comprehensive sequence validation by our expert application scientists.

Identification of PTMs and sequence variants.

Quantitative analysis of PTMs and sequence variants.

In less than two weeks, receive a comprehensive and PEAKS-based report.

Antibody Characterization

Service