I have been experiencing some problems trying to open mzXML files with mMass in Windows 7. I have been able to open the same files in XP and Mac OS X using the same versión of mMass but not in Windows 7. I have tried with different versions but the files cannot be opened, a window appears with the message: "Unable to open the document. Selected document is damaged or contains no data".

In the mmass.exe.log file I obtain the following

Exception in thread Thread-2:
Traceback (most recent call last):
  File "threading.pyo", line 552, in __bootstrap_inner
  File "threading.pyo", line 505, in run
  File "gui\main_frame.pyo", line 3745, in getDocumentScanList
  File "mspy\parser_mzxml.pyo", line 128, in scanlist
  File "xml\sax\expatreader.pyo", line 107, in parse
  File "xml\sax\xmlreader.pyo", line 119, in parse
  File "xml\sax\expatreader.pyo", line 111, in prepareParser
UnicodeEncodeError: 'ascii' codec can't encode character u'\xe1' in position 20: ordinal not in range(128)

Thank you

I'm analyzing ESI data that was converted with compassXport.

(Also, just so you know, I don't even run the MS myself...  I just give my sample to someone and get the file back.)

So when I open my file, I already have all peaks picked. Even tiny little ones. If I want to delete labels, it deletes the whole peak.
If I use the automatic peak picking tool, it doesn't change anything, whatever threshold I set. Is it supposed to delete labels for peaks under the threshold? Right now, whether I set a random high S/N ratio, an mid-height a.i. or a 50% relative intensity, it doesn't seem to do anything.

I run my laptop under Ubuntu, and mMass is the only way I can analyze my MS data from there, so I'd really like to be able to only label the peaks I want.

Thank you for any help!

This is a great and easy to use program that is much superior to the Bioanalyist 1.5 I'm using now. I can import files from Wiff format no problem and get them read in mMass.

Right now, my challenge is to deconvolute an ESI spectrum of a protein to get an accurate intact mass.

However, I can't seem to figure out how in mMass to deconvolute the charge envelope from the spectrum to get the result? It looks like this capability is in the software, but I can't figure out the steps.

Could I ask you to point me in the right direction? thanks,

Stef

(also, can't figure out how to post images to forum, or I would have included example data)

Thank you

As a general improvement, significant part of the mMass's processing core is now written in C programming language. Please follow the instructions in User's Guide if you are running mMass from source code or if you compile your own version.

As a first new feature, Mass to Formula tool has been added to calculate molecular compositions from given m/z value. The tool is designed according to the rules published by Kind T. and Feihn O. (BMC Bioinformatics 2007) In addition, generated formulae can be sent to several public databases to search for known compounds.

As a second new feature, Batch Processing tool has finally been added to apply multiple processing steps to multiple documents at once. Together with improved performance of math operations, this tool could now save you a lot of time in data processing.

Additional Math Operations have been added to average, sum or overlay all visible spectra.

Previously available Distance Measurement tool has been improved and renamed to Spectrum Ruler. In addition to other features, new possibilities to measure peak area or to calculate charge of a protein from ESI spectra have been added.

Complete list of changes:
---------------------

ADDED: Mass to Formula tool to generate molecular formula from given m/z value.
ADDED: Batch Processing tool to apply multiple processing steps to multiple documents at once.
ADDED: Minor axis ticks can be shown in spectrum canvas.
ADDED: Peak area can be calculated and shown by Spectrum Ruler tool.
ADDED: Protein charge state can be calculated and shown by Spectrum Ruler tool.
ADDED:Overlay function added to Math Operations panel.
ADDED: Combine All, Average All and Overlay All functions added to Math Operations panel.
ADDED: Photoshop-like method to see/enable just one document while hiding others.
ADDED: Sequence modifications can be applied specifically to N or C terminus.
ADDED: New view option to show/hide labels' Group name.
IMPROVED: Part of the mMass's processing core is now written in C.
IMPROVED: Faster calculation of Math Operations.
IMPROVED: Faster loading of single-scan documents from mzML, mzXML and mzData.
IMPROVED: Information shown by Spectrum Ruler tool can be set via application menu View.
IMPROVED: Drawing of individual peaks in pattern simulator can be disabled to speed up calculation.
FIXED: Multiple files selection in Open dialog.
FIXED: Application sometimes crashed when peaks were labeled with Sequence panel opened.

Could you tell me how to compile from source on Ubuntu (the Debian package does not fit)? I tried the setup.py, but it does not include any reference for Linux platform. Sorry for that dummy question, but I am not good at Python, although C is no problem.

Regards.

First of all, thank you very much for the wonderful software and for this forum space.

I have some *.ms mass spectra files from Agilent, and I would like to use it with mmass.. I read the user manual that I need some format such as mzXML, but I cannot for the life of me find a way to convert from *.ms to this format.. I've been doing a lot of googling with no luck... Can anybody point me out to the right direction? Thank you very much

Thank you very much for your very useful software

running build
running build_ext
building 'calculations' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -DNDEBUG -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -g -fPIC -I/usr/lib64/python2.7/site-packages/numpy/core/include/numpy -I/usr/include -I/usr/include/python2.7 -c calculations.c -o build/temp.linux-x86_64-2.7/calculations.o
calculations.c: In function ‘calculations_scaleAndShift’:
calculations.c:37:11: attention : assignment from incompatible pointer type
calculations.c: In function ‘calculations_filterPoints’:
calculations.c:146:11: attention : assignment from incompatible pointer type
gcc -pthread -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags build/temp.linux-x86_64-2.7/calculations.o -L/usr/lib64 -lpython2.7 -o build/lib.linux-x86_64-2.7/calculations.so
build/temp.linux-x86_64-2.7/calculations.o: In function `calculations_scaleAndShift':
/usr/local/logiciels/mMass/mspy/plot/calculations.c:44: undefined reference to `round'
/usr/local/logiciels/mMass/mspy/plot/calculations.c:45: undefined reference to `round'
collect2: ld a retourné 1 code d'état d'exécution
error: command 'gcc' failed with exit status 1

Can you help me to install mMass please.
Thank you a lot.

Several tools were added of modified to enable better analyses of natural peptides. It includes a database of more than 500 building blocks, additional sequence editor for custom-type sequences and a possibility to set sequence as being linear or cyclic. In addition to this, bunch of new fragmentation pathways were added to fragmentation module, including user-defined neutral losses or sequence scrambling. (Please make sure you place the monomers.xml file into your configs folder under MS Windows or Linux.)

If H/D exchange experiments is your primary work, you might find useful the new Envelope Fit tool. In general, it uses calculations of theoretical isotopic patterns and linear combination to determine deuterium incorporation by fitting calculated profiles into acquired data. As a result, you not only get the average incorporation of deuterium but a complete list of individual states with corresponding percentage as well. Since you can define what atoms to exchange, this module is not limited to H/D exchange only.

Using the Label Envelope tool set to "Monoisotopic Mass" you can determine monoisotopic mass of multiply charged proteins/peptides even if the real monoisotopic peak is not visible (see Senko M. et al. 1995 JASMS). Please note, that this feature works for regular protein/peptide sequences only.

Using the Measure Distances mouse tool you can now easily determine peak charge. Just measure distance between two isotopes and see corresponding charge value down in the bottom toolbar.

Complete list of changes:
---------------------

New: Additional Sequence Editor to define custom peptide sequence with non-standard amino acids.
New: Peptide sequence can be set as linear or cyclic.
New: N-terminal modifications can be saved in presets.
New: Internal monomer library with more that 500 building blocks according to NORINE database.
New: Monomer Library Editor to allow user-defined monomers and corresponding neutral losses.
New: Improved Peptide Fragmentation tool with more fragmentation pathways.
New: Gaussian smoothing filter.
New: Overall matched intensity is calculated and shown in Match panel and Sample Report.
New: Envelope Fit tool to determine heavy atoms exchange (e.g for HDX experiments).
New: Monoisotopic mass determination for large proteins with isotopically resolved envelope.
New: Charge state is shown in the bottom bar for Measure Distance tool and current difference.
New: Save All feature to save all opened documents at once.
New: Current document’s path is shown in Document Info panel.
New: Charge column is shown for annotations and sequence matches in Sample Report.
New: User’s Guide PDF is accessible via application menu Help.
Changed: Definition of the z-series ions according to Mascot.
Changed: Polished icons to better fit into OS X Lion.
Fixed: An issue with mzData time parameter.

Is there any option I should used to print a pdf in Hight resolution. (I would like to get a vectorial image)

Thank you a lot for this software.

If this feature is already implemented could you tell me how to get it, thank you very much.

I've just started using mMass. I find it an easy to use program that fulfills the requirements for semi-automatic data analysis. However, I have two small problems:
1) I would like to generate a library of sequences, since I very frequently need the same 40-50 ones. Although in the handbook (page 49) is stated "if you are using some sequences frequently, save them into mMass document as a sequence library.", I cannot find the corresponding option in the menues.
2) I would like to create several different presets for modifications, but whenever I try to do it from the window "Sequence modifications" and click over "Save as presets", I always become the same answer "Global modifications not found. Global modifications only can be saved in presets." If I go to the presets menu, I just can rename or delete the existing presets, but I cannot create new ones.

My mMass runs on Windos 7.

Many thanks in advance for your support,

Ana