Two working versions of findX

These latest findX versions (FINDX_BS3g_7ppm.py & FINDX_BS3g_20ppm.py) for use with the BS3 cross-linker can be found here (7ppm) and here (20 ppm).
If you're new to findX please view the manual. In order to run findX you must have Python version 2.7.2 installed on your machine.


In this version of findX I have:

• Fixed some bugs in MSMS mode.
• Introduced the possibility to run findX with isotope mixes other than 50%.
• Added a filter based on peak intensities.
• Improved the sensitivity for H12/D12 doublet verification.
• Either a stringent 7 ppm cut-off for doublet verification, or a more loose 20 ppm cut-off.

Please note that the distiller compatibility is still not full functional. Also, peak list files need to be prepared for findX being able to read them properly.


Please cite: Söderberg et al. (2012) Detection of crosslinks within and between proteins by LC-MALDI-TOFTOF and the software FINDX to reduce the MSMS-data to acquire for validation (DOI: 10.1371/journal.pone.0038927) if you use findX.

FINDX_BS3e.py

The latest findX software (FINDX_BS3e.py) for use with the BS3 cross-linker can be found here.

If you're new to findX please view the manual. In order to run findX you must have Python version 2.7.2 installed on your machine.

In this version of findX I have:

• Added support for Mascot Distiller output. Basically if you use Mascot Distiller to extract and process data from your MALDI mass spectrometer, and output it to .txt (comprehensive) or .mgf (mascot generic file) files then findX can now read the relevant information (peak masses and intensities).
• Added better control of the merging process in MS mode. You can now set a dedicated tolerance level for merging masses and a dedicated tolerance level for matching masses.

Please direct any questions or bugs either in the comment section below, or to findxlink@gmail.com. To make it easier to find the problem paste any error message received. And if you email then attach data files in use e.g. sequence file(s), peak lists (zipped) and FINDX_settings.txt.

findX blog premiere

Here is where you will find up to date versions of the findX software used to annotate masses found with MALDI mass spectrometry.