Data Analysis

Drawing on our experience in high-resolution 2D-gel based proteomics, Proteome Consult is proud to offer you a choice of high quality analytical services:

2D-Gel Image Analysis

Assembly of 2D-gel databases

Construction of 2D-gel databases using Melanie 3.0 (Swiss Institute for Bioinformatics) or ImageMasterTM 2D Platinum software package. Full matching information will be generated, i.e. each gel will be matched against each other in order to obtain the most complete set of spot groups possible. Consequently, you will be perfectly free to choose the classes (control, treatment, disease, sex, age, ...) you attribute the gels to during data evaluation.
Since each gel had been "reference gel" at one point during the matching routine, all protein spots which were found matching to a group for at least n-times (n=3, default) will be represented as a group within the matched proteome database. Proteome Consult has extensive experience in assembling large 2D-gel databases. We have successfully matched databases comprising >250 high resolution 2D-gels containing >106 spots without encountering a technological limit. No intermediate average gels need to be used.

High troughput image analysis

For all customers committed to obtained the best available spot quantification model as well as low processing times, Proteome Consult can offer to analyse 2D-gels by Ludesi AB 2D-gel analyser software. Please inquire to take advantage of our special rates for this service.

Getting a Quote

The working effort needed for 2D-gel matching strongly depends on parameters like gel to gel reproducibility, staining quality, number of spots, number and size of speckles and other artifacts, pattern reproducibility within the matchset (i.e. degree of variation due to treatment) and obviously the number of gels which need to be matched.
To submit an accurate quotation we require to obtain a selection comprising ~50% of all gels to be matched, however, at least one representative gel image (TIF) of each treatment class.

ImageMasterTM is a Trademark of Amersham Biosciences AB, Uppsala (Sweden)



MS-Data Analysis

Protein identification and sequencing

From raw-data processing to Mascot-searching, Proteome Consult offers expert data evaluation of ESI-MS-, Maldi-MS-, MS/MS- and Edman data.


Protein identification by analysis of MALDI MS-fingerprinting data can be performed starting from different stages of data processing. Refined mass lists may be either provided by the customer or assembled by Proteome Consult from unprocessed mass lists or MALDI-TOF-spectra according to specified criteria.
Within the framework of an analytical project raw data analysis can be performed for the Bruker Reflex/Ultraflex-series instruments.

Protein sequences

Protein sequences can be obtained from Edman-chromatograms, as well as from ESI-MS/MS- or MALDI-PSD-spektra. Within the framework of an analytical project ESI MS/MS or MALDI post scource decay data can be analyzed using raw-data of Micromass Q-TOF series and Bruker Reflex/Ultraflex-series instruments.

Mascot Searches

Mascot searches will be done in cooperation with a partner company bound by a confidentiality agreement, if required to address customer needs.

Software for data analysis

Proteome Consult can offer to develop software (Visual Basic, Perl, PHP) for customer specific data processing needs, please inquire.

Sending Data

Data may be submitted on CD-ROM, DVD, CompactFlash® card, MicroDrive® or may be made available for download on a website. Matched databases will be returned on media according to customer needs. Please specify your preferred storage medium. If no storage medium is specified, matched databases will be send on CD-ROM. All customer data will be treated as strictly confidential.

CompactFlash® is a registered Trademark of SanDisk Corp., Sunnyvale (USA)

MicroDrive® is a registered Trademark of Hitachi Global Storage Technologies, San José (USA)