PeptideIndexer: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/PeptideIndexer - from package: topp

You may install the required package with command apt-get install {package}
Error in other languages:
PeptideIndexer: bevel nie gevind nie
PeptideIndexer: comandă negăsită
PeptideIndexer: comando não encontrado
PeptideIndexer: commande introuvable
PeptideIndexer: command not found
PeptideIndexer: käsku ei ole
PeptideIndexer: không tìm thấy lệnh
PeptideIndexer: komanda nerasta
PeptideIndexer: Kommando nicht gefunden.
PeptideIndexer: kommandot finns inte
PeptideIndexer: komut yok
PeptideIndexer: nie znaleziono polecenia
PeptideIndexer: níor aimsíodh an t-ordú
PeptideIndexer: no se encontró la orden
PeptideIndexer: no s'ha trobat l'ordre
PeptideIndexer: opdracht niet gevonden
PeptideIndexer: parancs nem található
PeptideIndexer: perintah tidak ditemukan
PeptideIndexer: príkaz nenájdený
PeptideIndexer: příkaz nenalezen
PeptideIndexer: команда не найдена
PeptideIndexer: командата не е открита
PeptideIndexer: 命令找不到
PeptideIndexer: コマンドが見つかりません