Component of Mass Spectrometry-Based Proteomics Suite Software for Protein Data Interpretation biotools 2.2 > Enabling Life Science Tools Based on Mass Spectrometry size="-2">

As a central component of the PROTEINEER hardware and software suite, BioTools gives an unprecedented support to mass spectrometry-based proteomics and protein analysis. BioTools provides automated, user-defi ned routines for batch processing and screening, as well as interactive tools to extract in-depth structural information from MS and MS/MS data, including the RapiDeNovoٙ module for de novo sequencing. > Two major approaches for proteomics and protein analysis are common in modern protein science:1. Screening approaches that generate a high amount of data, from hundreds to thousands of peptide...

de novo sequencing with the added RapiDeNovo module yielding sequence results even from complex MS/MS spectra. > One major focus in protein chemistry is the identifi cation of unknown pro-teins from either 2D-gels or solutions. In the standard proteomics approach, the proteome is fractionated and pro- teins are displayed in a two dimen- sional gel (2DGE). Here individual proteins can be quantifi ed, picked as spotsӔ and digested with an enzyme such as trypsin. The characteristic pattern of proteolytic peptides, the peptide mass fi ngerprint (PMF), is then obtained by MALDI-TOF mass spectrometry...

Fig. 4: Workfl ow Administration by Result-driven Processing (WARP) approach. BioTools is in a core position triggering MS/MS acquisitions. added information is calculated (fi g. 6). The mass list of the predicted peptides can then be compared with the spectrum to create an increased sequence coverage. Screen for unmatched peptides in the sequence In most cases, not all of the peaks in the spectrum can be assigned to the identifi ed protein after database search. Reasons might be an insuffi -cient choice of optional modifi cations for database searching, point muta- tions or sequence errors,...

tion which gives exactly the same peptide as for the fi rst suggestion. Post-translational modifi cations (PTMs) are of major interest in pro- teomics. Usually, the database search results include hints for PTMs. How- ever, in many cases various possibilities for a PTM exist on a given sequence. Also, additional modifi cations may be present. BioTools provides the pos- sibility to localize the exact modifi ca-tion site based on MS/MS data.In a hit of beta-casein, a peptide sequence of FQSEE QQQTE DELQD K was found with a possible single phosphorylation. BioTools highlights this in blue in the...

Fig. 9: Identifi cation of a peptide phosphorylation site. a) Peak with a hint for phosphorylation from the database search. b) Calculation of the theoretical MS/MS spectra based on the two possible phospho-sites. c, d) Comparison of both calculated spectra with the MS/MS data: the visualization easily reveals the correct Ser-phosphorylation by a better sequence coverage. >

De novo sequencing using peak parking in combination with nanoLC-ion trap mass spectrometry Bruker Daltonics Application Note #LCMS-41, Protein identifi cation and beyond using a novel RapiDeNovo sequencing toolՕ Bruker Daltonics Application Note #LCMS-43, Identifi cation of proteins from Taxus baccata : A species with a non-sequenced genome The RapiDeNovo software for de novo Further Literature sequencing is further described in the application notes: Bruker Daltonics Application Note #MT-66/LCMS-37, De novo sequenc- ing of tryptic peptides using MALDI-TOF/TOF MS and nanoESI-ion trap MSՕ Bruker...

de novo sequencing is performed with the RapiDeNovo module. Subsequent MS-BLAST homology search is supported. BioTools features batch result reporting in MTP viewer and HTML format, and Մcopy and paste export of displayed items, e.g. spectra, sequence maps, and search results, into reports and offi ce documents. > ӕ Protein identifi cation is supported as a batch process, using peptide mass fi ngerprint (PMF), MALDI- and ESI-MS/MS data. Effective viewing and judgment of individual PMF and MS/MS results is possible giving interactive access to candidate lists, spectra, informa- tion from database...

BDALDE 09 04, LS-4 www.bdal.de www.bdal.com Bruker Daltonik GmbH Bruker Daltonics Inc. Bremen GermanyPhone +49 (421) 2205-0Fax +49 (421) 2205-104E-Mail [email protected] Billerica, MA ׷ USAPhone +1 (978) 663-3660Fax +1 (978) 667-5993E-Mail [email protected] See our website for worldwide sales and service contacts. >