FileFilter

Options

version

Version of the tool that generated this parameters file.

in_type

Input file type -- default: determined from file extension or content

rt

Retention time range to extract

mz

m/z range to extract (applies to ALL ms levels!)

int

Intensity range to extract

sort

Sorts the output according to RT and m/z.

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

sn

Write peaks with S/N > 'sn' values only

rm_pc_charge

Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!

pc_mz_range

MSn (n>=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag.

pc_mz_list

List of m/z values. If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept.

level

MS levels to extract

sort_peaks

Sorts the peaks according to m/z

no_chromatograms

No conversion to space-saving real chromatograms, e.g. from SRM scans

remove_chromatograms

Removes chromatograms stored in a file

remove_empty

Removes spectra and chromatograms without peaks.

mz_precision

Store base64 encoded m/z data using 32 or 64 bit precision

int_precision

Store base64 encoded intensity data using 32 or 64 bit precision

indexed_file

Whether to add an index to the file when writing

zlib_compression

Whether to store data with zlib compression (lossless compression)

masstime

Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)

lossy_mass_accuracy

Desired (absolute) m/z accuracy for lossy compression (e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy).

intensity

Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)

float_da

Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)

remove_zoom

Remove zoom (enhanced resolution) scans

remove_mode

Remove scans by scan mode

remove_activation

Remove MSn scans where any of its precursors features a certain activation method

remove_collision_energy

Remove MSn scans with a collision energy in the given interval

remove_isolation_window_width

Remove MSn scans whose isolation window width is in the given interval

select_zoom

Select zoom (enhanced resolution) scans

select_mode

Selects scans by scan mode

select_activation

Retain MSn scans where any of its precursors features a certain activation method

select_collision_energy

Select MSn scans with a collision energy in the given interval

select_isolation_window_width

Select MSn scans whose isolation window width is in the given interval

select_polarity

Retain MSn scans with a certain scan polarity

replace_pc_charge

Replaces in_charge with out_charge in all precursors.

similarity_threshold

Similarity threshold when matching MS2 spectra. (-1 = disabled).

rt

Retention tolerance [s] when matching precursor positions. (-1 = disabled)

mz

m/z tolerance [Th] when matching precursor positions. (-1 = disabled)

use_ppm_tolerance

If ppm tolerance should be used. Otherwise Da are used.

blacklist

True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept

q

Overall quality range to extract [0:1]

map

Non-empty list of maps to be extracted from a consensus (indices are 0-based).

map_and

Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')

blacklist

True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept

maps

Maps used for black/white list filtering

rt

Retention tolerance [s] for precursor to consensus feature position

mz

m/z tolerance [Th] for precursor to consensus feature position

use_ppm_tolerance

If ppm tolerance should be used. Otherwise Da are used.

charge

Charge range to extract

size

Size range to extract

remove_meta

Expects a 3-tuple (=3 entries in the list), i.e. <name> 'lt|eq|gt' <value>; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!

remove_hull

Remove hull from features.

remove_clashes

Remove features with id clashes (different sequences mapped to one feature)

keep_best_score_id

in case of multiple peptide identifications, keep only the id with best score

sequences_whitelist

Keep only features containing whitelisted substrings, e.g. features containing LYSNLVER or the modification (Oxidation). To control comparison method used for whitelisting, see 'id:sequence_comparison_method'.

sequence_comparison_method

Comparison method used to determine if a feature is whitelisted.

accessions_whitelist

keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN

remove_annotated_features

Remove features with annotations

remove_unannotated_features

Remove features without annotations

remove_unassigned_ids

Remove unassigned peptide identifications

rt

Retention tolerance [s] for precursor to id position

mz

m/z tolerance [Th] for precursor to id position

blacklist_imperfect

Allow for mismatching precursor positions (see 'id:blacklist')

max_intensity

maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.

auto_max_stdev_factor

parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev

auto_max_percentile

parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile

auto_mode

method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method

win_len

window length in Thomson

bin_count

number of bins for intensity values

min_required_elements

minimum number of elements required in a window (otherwise it is considered sparse)

noise_for_empty_window

noise value used for sparse windows

write_log_messages

Write out log messages in case of sparse windows or median in rightmost histogram bin

Views

FileFilter Std Output

The text sent to standard out during the execution of FileFilter.

FileFilter Error Output

The text sent to standard error during the execution of FileFilter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

• 02-download_and_analyze_raw_fileKNIME Hub
• Calculate_variable_DIA_windowsKNIME Hub
• DIAMetAlyzer_2.0OpenMS
• DIAMetAlyzer_2.0KNIME Hub
• DIAMetAlyzer_ABKNIME Forum
• Show all 6 workflows

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