Spectrum Mill

https://proteomics.broadinstitute.org/millhtml/
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Spectrum Mill is mass spectrometry proteomics software from the Broad Institute that provides tools...
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### Example Database References

Source: https://proteomics.broadinstitute.org/millhtml/faindex.htm

These examples show how different protein sequence databases can be referenced. They include specific database names and file paths, and some examples appear to be constructed to test for SQL injection vulnerabilities.

```sql
' RLIKE (SELECT (CASE WHEN (952=952) THEN 1 ELSE 0x28 END)) -- NCBInr.user 0'XOR(if(now()=sysdate(),sleep(15),0))XOR'ZNCBInr.user.1 0'XOR(if(now()=sysdate(),sleep(15),0))XOR'ZNCBInr.user 2dnTc1Z5')) OR 506=(SELECT 506 FROM PG_SLEEP(15))--NCBInr.user NCBInr.user' RLIKE (SELECT (CASE WHEN (336=336) THEN 1 ELSE 0x28 END)) -- NCBInr.user.1-1 OR 339=(SELECT 339 FROM PG_SLEEP(15))-- NCBInr.user.1-1) OR 344=(SELECT 344 FROM PG_SLEEP(15))-- NCBInr.user.1-1)) OR 250=(SELECT 250 FROM PG_SLEEP(15))-- NCBInr.user.1 NCBInr.user.15Z7BNXY9' OR 570=(SELECT 570 FROM PG_SLEEP(15))-- NCBInr.user.1CPTm9TfC')) OR 860=(SELECT 860 FROM PG_SLEEP(15))-- NCBInr.user.1I1HIBMhm') OR 351=(SELECT 351 FROM PG_SLEEP(15))-- NCBInr.user.1pqI8jDUA NCBInr.user.2 NCBInr.user.@@RqVXy NCBInr.user NCBInr.user0'XOR(if(now()=sysdate(),sleep(15),0))XOR'Z NCBInr.user0KEVKZkP NCBInr.user4Q0RmhL5' OR 435=(SELECT 435 FROM PG_SLEEP(15))-- NCBInr.userJTQs4uOt') OR 740=(SELECT 740 FROM PG_SLEEP(15))-- NCBInr.userxuEEO84F')) OR 529=(SELECT 529 FROM PG_SLEEP(15))-- PAhomologoussequences.acc.1-1 OR 358=(SELECT 358 FROM PG_SLEEP(15))-- PAhomologoussequences.acc.1-1) OR 161=(SELECT 161 FROM PG_SLEEP(15))-- PAhomologoussequences.acc.1-1)) OR 875=(SELECT 875 FROM PG_SLEEP(15))-- PAhomologoussequences.acc.1 PAhomologoussequences.acc.10RhMZSrJ' OR 22=(SELECT 22 FROM PG_SLEEP(15))-- PAhomologoussequences.acc.1E9zMSiKs')) OR 151=(SELECT 151 FROM PG_SLEEP(15))-- PAhomologoussequences.acc.1qDIdMFEL PAhomologoussequences.acc.1Zuzs7pwg') OR 636=(SELECT 636 FROM PG_SLEEP(15))-- PAhomologoussequences.acc.2 PAhomologoussequences.acc.@@RamhS PAhomologoussequences.acc PAVenom_Arachno PAVenom_SmG PAVenom_Um pIiqP6kj') OR 170=(SELECT 170 FROM PG_SLEEP(15))--NCBInr.user SwissProt.Ecoli twAM6h7o' OR 304=(SELECT 304 FROM PG_SLEEP(15))--NCBInr.user UniProt.human.20141017.RNFISnr.150contams UniProt.human.20171228.RISnrNF.553smORFs.264contams.fasta UniProt.human.20210902.RInrNF.602contams.fasta UniProt.human.mouse.20141017.RNFISnr.150contams UniProt.human.mouse.20171228.RISnrNF.553smORFs.264contams.fasta UniProt.human.NFISnr.contams UniProt.mouse.20141017.RNFISnr.150contams UniProt.mouse.20171228.RISnrNF.553smORFs.264contams.fasta UniProt.mouse.NFISnr.contams UniProt.RattusNorvegicus.NFISnr.contams UniProt.Yeast.NFISnr.contamsS48 UniProtContams_602_20201023.fasta.1 UniProtContams_602_20201023.fasta YgpRfoJFNCBInr.user
```

--------------------------------

### protchem.js Example

Source: https://proteomics.broadinstitute.org/millhtml/SM_instruct/servadmn.htm

Example of JavaScript code from protchem.js related to displaying variable modification localization choices.

```javascript
E:\SpectrumMill\millhtml\SM_js\protChem.js.
protchem.js
displayVariableModificationLocalizationAAChoices()
document.writeln ("<option>
<option>")
```

--------------------------------

### Example entry for msprod in urlsElementalComposition.txt

Source: https://proteomics.broadinstitute.org/millhtml/sm_instruct/servadmn.htm

This example demonstrates the two-line format for an entry in the urlsElementalComposition.txt file, specifying the program name and the URL for linking elemental compositions.

```text
msprod
../millbin/MSISO?distribution_type=Elemental+Composition
```

--------------------------------

### Get CGI Timeout

Source: https://proteomics.broadinstitute.org/millhtml/SM_instruct/servadmn.htm

Example of displaying the current CGI timeout setting for the Spectrum Mill Web site using the getcgi.vbs script with CScript.

```batch
E:\SpectrumMill\milladmin> wscript getcgi.vbs
```

--------------------------------

### SMSRM.config Example

Source: https://proteomics.broadinstitute.org/millhtml/SM_instruct/servadmn.htm

Example line from the SMSRM.config file showing the maxConcurrentTasks setting.

```xml
<provider hostname="localhost" available="true" maxConcurrentTasks="3" minRequiredTaskMemoryGb="2">
```

--------------------------------

### Running FAindex from the command line

Source: https://proteomics.broadinstitute.org/millhtml/SM_instruct/faman.htm

Example of how to run the faindex.cgi program from an MS-DOS command prompt to create index files for a database.

```bash
C:\ > D:
D:\ > E:\SpectrumMill\millbin\faindex.cgi NCBInr
```

--------------------------------

### Enzymatic Digest Rule Example

Source: https://proteomics.broadinstitute.org/millhtml/SM_instruct/servadmn.htm

Example entry for trypsin in the enzymes.txt file.

```text
Trypsin  
KR  
P  
C 
```
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