LipidXplorer Reference - Revision history

B.hossen at 12:23, 26 August 2026

2026-08-26T12:23:04Z

B.hossen: /* Machine specific settings */

2026-08-17T14:34:41Z

Machine specific settings

B.hossen: /* Machine specific settings */

2026-08-17T14:33:59Z

Machine specific settings

B.hossen: /* Import of MS/MS spectra using .dta;removed in LipidXplorer 1.2.8 /

2026-08-17T14:28:32Z

Import of MS/MS spectra using *.dta;removed in LipidXplorer 1.2.8

B.hossen: /* Import of peak lists of MS/MS in .dta format and MS in .csv; removed in LipidXplorer 1.2.8 */

2026-08-17T14:27:53Z

Import of peak lists of MS/MS in *.dta format and MS in *.csv; removed in LipidXplorer 1.2.8

B.hossen at 14:26, 17 August 2026

2026-08-17T14:26:46Z

Jacobo.miranda: /* Machine specific settings */

2019-10-01T12:19:41Z

Machine specific settings

Jacobo.miranda: /* Importing PIS/NLS */

2019-08-13T08:08:49Z

Importing PIS/NLS

Jacobo.miranda: /* Import of MS/MS spectra using .dta /

2019-08-13T08:08:27Z

Import of MS/MS spectra using *.dta

Jacobo.miranda: /* Import of MS1 information using .csv file format /

2019-08-13T08:08:14Z

Import of MS1 information using *.csv file format

@@ Line 22: / Line 22: @@
 ==== *.mzML ====
-mzXML is a XML (eXtensible Markup Language) based common file format for mass spectrometric data [http://onlinelibrary.wiley.com/doi/10.1002/pmic.200890049/abstract;jsessionid=DFF64D7FEB924A67A29D91EDC1A18261.d01t03?systemMessage=Wiley+Online+Library+will+be+disrupted+on+9+June+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance Deutsch EW (2008). "mzML: A single, unifying data format for mass spectrometer output". Proteomics 8 (14): 2776–7.]. It should replace the commonly used file formats *.mzData and *.mzXML. See [http://en.wikipedia.org/wiki/Mass_spectrometry_data_format Wikipedia on mass spectrometry data formats] for more information.
+mzML is a XML (eXtensible Markup Language) based common file format for mass spectrometric data [http://onlinelibrary.wiley.com/doi/10.1002/pmic.200890049/abstract;jsessionid=DFF64D7FEB924A67A29D91EDC1A18261.d01t03?systemMessage=Wiley+Online+Library+will+be+disrupted+on+9+June+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance Deutsch EW (2008). "mzML: A single, unifying data format for mass spectrometer output". Proteomics 8 (14): 2776–7.]. It should replace the commonly used file formats *.mzData and *.mzXML. See [http://en.wikipedia.org/wiki/Mass_spectrometry_data_format Wikipedia on mass spectrometry data formats] for more information.
 ==== Import of peak lists of MS/MS in *.dta format and MS in *.csv; ====

@@ Line 168: / Line 168: @@
 * On Orbitrap machines we discovered a decrease of 50,000 from m/z 300 to m/z 1200. This gradient value increases the accuracy of the spectra alignment.
 '''Frequency filter:''' a minimum frequency for a peak appearing in all associated scans, the value should be between 0 and 1
 '''MS1 offset:''' All MS1 m/z values will be shifted by this value.

← Older revision		Revision as of 14:33, 17 August 2026
Line 168:		Line 168:
	* On Orbitrap machines we discovered a decrease of 50,000 from m/z 300 to m/z 1200. This gradient value increases the accuracy of the spectra alignment.		* On Orbitrap machines we discovered a decrease of 50,000 from m/z 300 to m/z 1200. This gradient value increases the accuracy of the spectra alignment.

		+	'''Frequency filter:''' a minimum frequency for a peak appearing in all associated scans, the value should be between 0 and 1

	'''MS1 offset:''' All MS1 m/z values will be shifted by this value.		'''MS1 offset:''' All MS1 m/z values will be shifted by this value.

@@ Line 74: / Line 74: @@
 </pre>
-===== Import of MS/MS spectra using *.dta;removed in LipidXplorer 1.2.8  =====
+===== Import of MS/MS spectra using *.dta; =====
 Many mass spectrometers software are able to generate a peak lists of MS/MS spectra and save them in the *.dta file format. It contains a peak list table, which has as head the precursor mass in m/z and its charge and the tables content are masses with the according intensity.

@@ Line 24: / Line 24: @@
 mzXML is a XML (eXtensible Markup Language) based common file format for mass spectrometric data [http://onlinelibrary.wiley.com/doi/10.1002/pmic.200890049/abstract;jsessionid=DFF64D7FEB924A67A29D91EDC1A18261.d01t03?systemMessage=Wiley+Online+Library+will+be+disrupted+on+9+June+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance Deutsch EW (2008). "mzML: A single, unifying data format for mass spectrometer output". Proteomics 8 (14): 2776–7.]. It should replace the commonly used file formats *.mzData and *.mzXML. See [http://en.wikipedia.org/wiki/Mass_spectrometry_data_format Wikipedia on mass spectrometry data formats] for more information.
-==== Import of peak lists of MS/MS in *.dta format and MS in *.csv; removed in LipidXplorer 1.2.8====
+==== Import of peak lists of MS/MS in *.dta format and MS in *.csv; ====
 As an easy way to make the functionality of LipidXplorer available for a wide range of mass spectrometric platforms is to provide the ability to import pre-processed peak-lists. Many vendors enable the functionality in their software to create *.dta files of MS/MS Spectra. In many instances one might be interested to import also the pre-processed peaklist of the MS1 which we support with the widely used *.csv file format. Both text file formats should be reasonable available as alternative for *.mzXml. For the import of *.dta and *.csv files, some pre-conditions have to met: The import files have to be given in a certain directory structure, which is:

← Older revision		Revision as of 14:26, 17 August 2026
Line 23:		Line 23:

	mzXML is a XML (eXtensible Markup Language) based common file format for mass spectrometric data [http://onlinelibrary.wiley.com/doi/10.1002/pmic.200890049/abstract;jsessionid=DFF64D7FEB924A67A29D91EDC1A18261.d01t03?systemMessage=Wiley+Online+Library+will+be+disrupted+on+9+June+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance Deutsch EW (2008). "mzML: A single, unifying data format for mass spectrometer output". Proteomics 8 (14): 2776–7.]. It should replace the commonly used file formats .mzData and .mzXML. See [http://en.wikipedia.org/wiki/Mass_spectrometry_data_format Wikipedia on mass spectrometry data formats] for more information.		mzXML is a XML (eXtensible Markup Language) based common file format for mass spectrometric data [http://onlinelibrary.wiley.com/doi/10.1002/pmic.200890049/abstract;jsessionid=DFF64D7FEB924A67A29D91EDC1A18261.d01t03?systemMessage=Wiley+Online+Library+will+be+disrupted+on+9+June+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance Deutsch EW (2008). "mzML: A single, unifying data format for mass spectrometer output". Proteomics 8 (14): 2776–7.]. It should replace the commonly used file formats .mzData and .mzXML. See [http://en.wikipedia.org/wiki/Mass_spectrometry_data_format Wikipedia on mass spectrometry data formats] for more information.
−
−	~~==== *.mzXML ====~~
−
−	mzXML is a XML (eXtensible Markup Language) based common file format for mass spectrometric data. [Pedrioli PG et al., Nat. Biotechnol. 22 (11): 1459, 66 [http://dx.doi.org/10.1038/nbt1031 doi]) (Lin SM et al., Expert review of proteomics 2 (6): 839, 45, [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17342793 PMID])
−
−	''LipidXplorer provides automatic conversation of data from ThermoFinnigan (Orbitrap) and Applied Biosystems (QStar) provided that the instruments software is installed on the same computer as LipidXplorer.''

	==== Import of peak lists of MS/MS in .dta format and MS in .csv; removed in LipidXplorer 1.2.8====		==== Import of peak lists of MS/MS in .dta format and MS in .csv; removed in LipidXplorer 1.2.8====

@@ Line 154: / Line 154: @@
 '''resolution:''' the resolution of the mass spectrometer in MS and MS/MS mode.
 *This value is used in the import for the spectra averaging and alignment. Both algorithms consider m/z values as equal if they are closer than the resolution allows.
+*Value given here defines resolution at the smallest m/z value of a give m/z range. Resolution will be computed according to slope given in "resolution gradient".
 '''tolerance:''' The tolerance value is the error LipidXplorer allows for a lipid to be identified.

@@ Line 128: / Line 128: @@
 The tab contains various possibilities of specifying mass spectrometric attributes. The configurations are stored in an *.ini file. There is a standard *.ini file provided, but by pressing 'Browse' next to the *.ini file, the user can select an own file.
-====Importing PIS/NLS====
+====Importing PIS/NLS; removed in LipidXplorer 1.2.8====
 Importing PIS/NLS spectra is done by checking "PIS spectra" on the Import Source panel of LipidXplorer. If this is not checked the spectra are not imported properly.

@@ Line 60: / Line 60: @@
 The names of the samples occurring in LipidXplorer are the names of the sample directories.
-===== Import of MS1 information using *.csv file format  =====
+===== Import of MS1 information using *.csv file format; removed in LipidXplorer 1.2.8=====
 A *.csv file is a comma separated file, i.e. every line in the file contains data which is separated by commas. LipidXplorer will solely recognize *.csv files for importing survey scan information(the MS experiment data) in the following format:
@@ Line 78: / Line 78: @@
 .5908,35523.1
 .5044,107847.3
 </pre>
 ===== Import of MS/MS spectra using *.dta  =====

LipidXplorer Reference - Revision history

B.hossen at 12:23, 26 August 2026

B.hossen: /* Machine specific settings */

B.hossen: /* Machine specific settings */

B.hossen: /* Import of MS/MS spectra using *.dta;removed in LipidXplorer 1.2.8 */

B.hossen: /* Import of peak lists of MS/MS in *.dta format and MS in *.csv; removed in LipidXplorer 1.2.8 */

B.hossen at 14:26, 17 August 2026

Jacobo.miranda: /* Machine specific settings */

Jacobo.miranda: /* Importing PIS/NLS */

Jacobo.miranda: /* Import of MS/MS spectra using *.dta */

Jacobo.miranda: /* Import of MS1 information using *.csv file format */

B.hossen: /* Import of MS/MS spectra using .dta;removed in LipidXplorer 1.2.8 /

B.hossen: /* Import of peak lists of MS/MS in .dta format and MS in .csv; removed in LipidXplorer 1.2.8 */

Jacobo.miranda: /* Import of MS/MS spectra using .dta /

Jacobo.miranda: /* Import of MS1 information using .csv file format /