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clochardM33

PLGS Threshold Inspector Command Line Interface

Applicable to v2.1 onwards supports command line arguments.
If the command line is used:
• processing starts immediately,
• all the available thresholds are selected,
• the application closes when processing is complete, and
• a csv file is created containing the ‘best’ threshold settings.

If a raw file has already been processed then the previous time range and thresholds are used. The previous data is not overwritten.

Argument Syntax
Name_1 | Value_1, Name_2 | Value_2, Name_3 | Value_3,etc etc Name_N | Value_N
Name Value is separated by the pipe character |

Argument sets are comma separated

Strings cannot contain comma characters

Strings do not need to be wrapped in double quotes

If starting from cmd prompt the whole argument line should be wrapped in one set of double quotes.
For example: \PLGSThresholdInspector.exe “Name_1 | Value_1, Name_2 | Value_2”

Parsing rules are: Split by comma, Split by pipe, remove double quotes, remove leading and trailing spaces.

Arguments

If any arguments are used the application operates as though the command line is in use.

Arguments are case sensitive and can be in any order.

All arguments are optional.

If an argument is not passed in the default value is that used by the application in standalone operation.

For example the locations of the database may be passed in, but if not the location specified the last time the application ran is used.

Location_RawFile
String
The full path of the input raw file.
For example: C:\MassLynx\Default.pro\Data\Example.raw

BestT_FileName
String
The full path, including filename and file extension) of output file containing the ‘best’ thresholds.
If not specified the file is written to {App folder}\PLGSTI_BestT.csv

Hide_UI
Boolean string. Pass in either True or False
If true the UI is minimized as the processing starts. The UI always appears in the start bar and can be resized by the user at any time. It is equivalent to selecting minimize from the form’s title bar.

Location_FastA
String
Full path of the database file.

Location_IAParam
String
Full path of the IAParameters file

Location_Apex
String
Full path of the Apex exe

Location_Peptide3D
String
Full path of the Peptide3d exe

Location_IADB
String
Full path of the IADB exe

TimeStart
Single
Start time for processing. Only used if the file has not already been processed by PLGSTI

TimeStop
Single
Stop time for processing. Only used if the file has not already been processed by PLGSTI

LockMassZ1_Use
Boolean string. Pass in either True or False
If True a LockMass value for Z1 is passed to Apex

LockMassZ1_Value
String. Numeric value passed in as text
The value of Z1 LockMass passed to Apex

LockMassZ2_Use
Boolean string. Pass in either True or False
If True a LockMass value for Z2 is passed to Apex

LockMassZ2_Value
String. Numeric value passed in as text
The value of Z2 LockMass passed to Apex

LockMass_Tolerance
Double
The value of LockMass tolerance passed to Apex

ThresholdClusterLevel
Single. 0 to 1
The % of thresholds rejected when determining the ‘best’ threshold.
For example to keep thresholds within 10% of the maximum number pass in a value of 0.9

‘Best’ Thresholds

The ‘best’ threshold is determined by a simple sort and rearrangement of the results.

The ‘best’ value will always be one of the processed thresholds; it is not interpolated.

The ‘best’ value is only best in so much as it comes out of the algorithm below. It represents the highest value of LE and HE that gives results within a specified percentage of the highest number of proteins measured.

The higher the value of LE and HE used in real processing the shorter the processing times.

Algorithm

Find the largest number of (green) proteins.

Keep all thresholds that are above Max * ThresholdClusterLevel

Only keep all thresholds that have the same LE as the highest value of LE

Keep the threshold that has the highest value of HE

Output File
4 lines.

  1. Header. First character is ;
  2. Raw file name. First character is ;
  3. LE Comma separated from ‘best’ LE value
  4. HE Comma separated from ‘best’ HE value
    For example:
    ;PLGSTI Best Value
    ;From rawfile: C:\MassLynx\Default.pro\Data\Example.raw
    LE,200
    HE,50

Example Sort
This data reduces to a best threshold of LE 250, HE 50 using the algorithm above.

LE HE Protein Count Green
125 50 578
200 50 577
150 50 575
200 25 572
50 50 570
250 50 568
250 25 567
75 50 565
100 50 562
150 25 558
100 25 552
125 25 548
200 10 523
250 10 515
50 75 514
75 25 514
75 75 510
200 75 507
125 75 506
150 75 506
100 75 505
150 10 504
250 75 497
125 10 484
50 100 448
250 100 447
200 100 446
75 100 446
150 100 446
125 100 443
100 100 441
100 10 433
50 25 427
75 10 228
50 10 65

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